[gentoo-commits] proj/sci:ccp4 commit in: sci-libs/cctbx/files/2013.02.27.0005/, sci-libs/cctbx/files/2012.05.08.2305/, ...

[Justin Lecher]

commit:     4dcc9136254923ef49146f459eb013152c907372
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Jun  1 16:49:03 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Jun  1 16:49:03 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=4dcc9136

sci-libs/cctbx: Version Bump

Package-Manager: portage-2.2.0_alpha177

---
 sci-libs/cctbx/ChangeLog                           |  218 ++++
 sci-libs/cctbx/cctbx-2012.05.08.2305.ebuild        |   81 ++
 sci-libs/cctbx/cctbx-2013.02.27.0005.ebuild        |   81 ++
 .../0001-remove-hardcoded-libtbx_build-env.patch   |   24 +
 .../0002-fix-opengl-header-missing-gltbx.patch     |   51 +
 ...0003-correct-paths-in-dispatcher-creation.patch |   85 ++
 ...ream-fix-for-declaration-errors-in-gcc4.7.patch |  442 ++++++++
 .../0005-fix-for-gcc4.7-compilation-error.patch    |   83 ++
 ...-for-system-libs-installtarget-and-prefix.patch | 1080 +++++++++++++++++++
 .../0007-adding-shlib-versioning.patch             |  208 ++++
 .../0008-Fix-to-skip-pycbf-build.patch             |   52 +
 .../0009-build-libann-statically.patch             |   27 +
 .../2012.05.08.2305/0010-adding-setup_py.patch     |  662 ++++++++++++
 ...011-fix-missing-python-lib-during-linking.patch |   47 +
 ...12-fix-to-remove-cctbx.python-interpreter.patch |   29 +
 ...o-support-LDFLAGS-in-use_enviroment_flags.patch |   90 ++
 .../0014-Fix-to-append-CPPFLAGS-to-CXXFLAGS.patch  |   21 +
 .../0016-autogenerate-pkgconfig-files.patch        |  305 ++++++
 .../0017-Fix-to-use-systems-include-path.patch     |  128 +++
 ...018-Fix-to-skip-build-of-clipper-examples.patch |   52 +
 .../files/2012.05.08.2305/0101-system-cbf.patch    |   16 +
 .../2012.05.08.2305/0101-system-clipper.patch      |  185 ++++
 .../files/2012.05.08.2305/0102-dontstrip.patch     |   25 +
 .../0001-remove-hardcoded-libtbx_build-env.patch   |   24 +
 .../0002-fix-opengl-header-missing-gltbx.patch     |   51 +
 ...0003-correct-paths-in-dispatcher-creation.patch |   86 ++
 ...-for-system-libs-installtarget-and-prefix.patch | 1099 ++++++++++++++++++++
 .../0007-adding-shlib-versioning.patch             |  208 ++++
 .../0008-Fix-to-skip-pycbf-build.patch             |   52 +
 .../0009-build-libann-statically.patch             |   27 +
 .../2013.02.27.0005/0010-adding-setup_py.patch     |  662 ++++++++++++
 ...011-fix-missing-python-lib-during-linking.patch |   47 +
 ...12-fix-to-remove-cctbx.python-interpreter.patch |   20 +
 ...o-support-LDFLAGS-in-use_enviroment_flags.patch |   90 ++
 .../0014-Fix-to-append-CPPFLAGS-to-CXXFLAGS.patch  |   21 +
 .../0016-autogenerate-pkgconfig-files.patch        |  305 ++++++
 .../0017-Fix-to-use-systems-include-path.patch     |  128 +++
 ...018-Fix-to-skip-build-of-clipper-examples.patch |   52 +
 .../files/2013.02.27.0005/0101-system-cbf.patch    |   16 +
 .../2013.02.27.0005/0101-system-clipper.patch      |  185 ++++
 .../2013.02.27.0005/0101-system-libccp4.patch      |   15 +
 .../files/2013.02.27.0005/0102-dontstrip.patch     |   25 +
 .../2013.02.27.0005/0103-respect-cflags.patch      |   60 ++
 sci-libs/cctbx/metadata.xml                        |   18 +
 44 files changed, 7183 insertions(+)

diff --git a/sci-libs/cctbx/ChangeLog b/sci-libs/cctbx/ChangeLog
new file mode 100644
index 0000000..949d710
--- /dev/null
+++ b/sci-libs/cctbx/ChangeLog
@@ -0,0 +1,218 @@
+# ChangeLog for sci-libs/cctbx
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/cctbx/ChangeLog,v 1.33 2013/03/19 07:07:15 jlec Exp $
+
+*cctbx-2013.02.27.0005 (01 Jun 2013)
+*cctbx-2012.05.08.2305 (01 Jun 2013)
+
+  01 Jun 2013; Justin Lecher <jlec@g.o> +cctbx-2012.05.08.2305.ebuild,
+  +cctbx-2013.02.27.0005.ebuild,
+  +files/2012.05.08.2305/0001-remove-hardcoded-libtbx_build-env.patch,
+  +files/2012.05.08.2305/0002-fix-opengl-header-missing-gltbx.patch,
+  +files/2012.05.08.2305/0003-correct-paths-in-dispatcher-creation.patch,
+  +files/2012.05.08.2305/0004-upstream-fix-for-declaration-errors-in-gcc4.7.pat
+  ch, +files/2012.05.08.2305/0005-fix-for-gcc4.7-compilation-error.patch,
+  +files/2012.05.08.2305/0006-options-for-system-libs-installtarget-and-prefix.
+  patch, +files/2012.05.08.2305/0007-adding-shlib-versioning.patch,
+  +files/2012.05.08.2305/0008-Fix-to-skip-pycbf-build.patch,
+  +files/2012.05.08.2305/0009-build-libann-statically.patch,
+  +files/2012.05.08.2305/0010-adding-setup_py.patch,
+  +files/2012.05.08.2305/0011-fix-missing-python-lib-during-linking.patch,
+  +files/2012.05.08.2305/0012-fix-to-remove-cctbx.python-interpreter.patch,
+  +files/2012.05.08.2305/0013-fix-to-support-LDFLAGS-in-use_enviroment_flags.pa
+  tch, +files/2012.05.08.2305/0014-Fix-to-append-CPPFLAGS-to-CXXFLAGS.patch,
+  +files/2012.05.08.2305/0016-autogenerate-pkgconfig-files.patch,
+  +files/2012.05.08.2305/0017-Fix-to-use-systems-include-path.patch,
+  +files/2012.05.08.2305/0018-Fix-to-skip-build-of-clipper-examples.patch,
+  +files/2012.05.08.2305/0101-system-cbf.patch,
+  +files/2012.05.08.2305/0101-system-clipper.patch,
+  +files/2012.05.08.2305/0102-dontstrip.patch,
+  +files/2013.02.27.0005/0001-remove-hardcoded-libtbx_build-env.patch,
+  +files/2013.02.27.0005/0002-fix-opengl-header-missing-gltbx.patch,
+  +files/2013.02.27.0005/0003-correct-paths-in-dispatcher-creation.patch,
+  +files/2013.02.27.0005/0006-options-for-system-libs-installtarget-and-prefix.
+  patch, +files/2013.02.27.0005/0007-adding-shlib-versioning.patch,
+  +files/2013.02.27.0005/0008-Fix-to-skip-pycbf-build.patch,
+  +files/2013.02.27.0005/0009-build-libann-statically.patch,
+  +files/2013.02.27.0005/0010-adding-setup_py.patch,
+  +files/2013.02.27.0005/0011-fix-missing-python-lib-during-linking.patch,
+  +files/2013.02.27.0005/0012-fix-to-remove-cctbx.python-interpreter.patch,
+  +files/2013.02.27.0005/0013-fix-to-support-LDFLAGS-in-use_enviroment_flags.pa
+  tch, +files/2013.02.27.0005/0014-Fix-to-append-CPPFLAGS-to-CXXFLAGS.patch,
+  +files/2013.02.27.0005/0016-autogenerate-pkgconfig-files.patch,
+  +files/2013.02.27.0005/0017-Fix-to-use-systems-include-path.patch,
+  +files/2013.02.27.0005/0018-Fix-to-skip-build-of-clipper-examples.patch,
+  +files/2013.02.27.0005/0101-system-cbf.patch,
+  +files/2013.02.27.0005/0101-system-clipper.patch,
+  +files/2013.02.27.0005/0101-system-libccp4.patch,
+  +files/2013.02.27.0005/0102-dontstrip.patch,
+  +files/2013.02.27.0005/0103-respect-cflags.patch, +metadata.xml:
+  Version Bump
+
+  19 Mar 2013; Justin Lecher <jlec@g.o> cctbx-2010.03.29.2334-r7.ebuild:
+  Use more functions from new python eclasses, fixes double prefix on PREFIX
+
+  17 Mar 2013; Justin Lecher <jlec@g.o> cctbx-2010.03.29.2334-r6.ebuild,
+  cctbx-2010.03.29.2334-r7.ebuild:
+  Add missing multilib.eclass
+
+*cctbx-2010.03.29.2334-r7 (17 Mar 2013)
+
+  17 Mar 2013; Justin Lecher <jlec@g.o>
+  +cctbx-2010.03.29.2334-r7.ebuild, metadata.xml:
+  Move to new python eclasses, log all file removals; bump to EAPI=5;add
+  missing die; use usex instead of custom check_use
+
+  19 Oct 2012; Justin Lecher <jlec@g.o> cctbx-2010.03.29.2334-r6.ebuild:
+  Remove virtual/fortran and always call fortran-2_pkg_setup as intend by the
+  updated fortran-2.eclass
+
+  18 Oct 2012; Justin Lecher <jlec@g.o> cctbx-2010.03.29.2334-r6.ebuild:
+  Remove virtual/fortran and always call fortran-2_pkg_setup as intend by the
+  updated fortran-2.eclass
+
+  06 Sep 2012; Justin Lecher <jlec@g.o> cctbx-2010.03.29.2334-r6.ebuild:
+  Use bundled scons on prefix, #391377
+
+  26 Aug 2012; Justin Lecher <jlec@g.o>
+  -cctbx-2010.03.29.2334-r3.ebuild, -cctbx-2010.03.29.2334-r4.ebuild,
+  -cctbx-2010.03.29.2334-r5.ebuild:
+  Drop old
+
+  19 Jun 2012; Justin Lecher <jlec@g.o>
+  +files/2010.03.29.2334-gcc-4.7.patch, cctbx-2010.03.29.2334-r6.ebuild:
+  Add fix for gcc-4.7
+
+  14 Jun 2012; Jeff Horelick <jdhore@g.o>
+  cctbx-2010.03.29.2334-r6.ebuild:
+  marked x86 per bug 413815
+
+  23 May 2012; Agostino Sarubbo <ago@g.o>
+  cctbx-2010.03.29.2334-r6.ebuild:
+  Stable for amd64, wrt bug #413815
+
+  10 Feb 2012; Markos Chandras <hwoarang@g.o>
+  cctbx-2010.03.29.2334-r3.ebuild, cctbx-2010.03.29.2334-r4.ebuild,
+  cctbx-2010.03.29.2334-r5.ebuild, cctbx-2010.03.29.2334-r6.ebuild:
+  Update Boost dependencies. Thanks to Arfrever
+
+*cctbx-2010.03.29.2334-r6 (10 Feb 2012)
+
+  10 Feb 2012; Justin Lecher <jlec@g.o>
+  +cctbx-2010.03.29.2334-r6.ebuild:
+  Add fixes for boost-1.48 and its PyABI specific libs, #401393
+
+*cctbx-2010.03.29.2334-r5 (04 Dec 2011)
+
+  04 Dec 2011; Justin Lecher <jlec@g.o>
+  +cctbx-2010.03.29.2334-r5.ebuild:
+  Create soname symlink, streamelined find and delete of unwanted files
+
+  07 Oct 2011; Justin Lecher <jlec@g.o> cctbx-2010.03.29.2334-r3.ebuild,
+  cctbx-2010.03.29.2334-r4.ebuild, metadata.xml:
+  Added [python] to dep on dev-libs/boost
+
+  21 Jun 2011; Justin Lecher <jlec@g.o> cctbx-2010.03.29.2334-r3.ebuild,
+  cctbx-2010.03.29.2334-r4.ebuild:
+  Add dependency on virtual/fortran
+
+  21 Jun 2011; Justin Lecher <jlec@g.o> cctbx-2010.03.29.2334-r3.ebuild,
+  cctbx-2010.03.29.2334-r4.ebuild:
+  Added fortran-2.eclass support
+
+*cctbx-2010.03.29.2334-r4 (10 Apr 2011)
+
+  10 Apr 2011; Justin Lecher <jlec@g.o>
+  +files/2010.03.29.2334-gcc-4.6.patch, +cctbx-2010.03.29.2334-r4.ebuild:
+  Fix changes in gcc-4.6
+
+  24 Jan 2011; Justin Lecher <jlec@g.o>
+  -cctbx-2010.03.29.2334-r1.ebuild:
+  Removed old
+
+  23 Jan 2011; Thomas Kahle <tomka@g.o> cctbx-2010.03.29.2334-r3.ebuild:
+  x86 stable per bug 351765
+
+  16 Jan 2011; Markos Chandras <hwoarang@g.o>
+  cctbx-2010.03.29.2334-r3.ebuild:
+  Stable on amd64 wrt bug #351765
+
+  16 Jan 2011; Kacper Kowalik <xarthisius@g.o>
+  cctbx-2010.03.29.2334-r3.ebuild:
+  marked ~ppc wrt #303931
+
+  15 Jan 2011; Justin Lecher <jlec@g.o>
+  -cctbx-2009.11.01.0123-r1.ebuild, -cctbx-2010.03.29.2334-r2.ebuild:
+  Removed old
+
+  15 Jan 2011; Justin Lecher <jlec@g.o>
+  files/2010.03.29.2334-boost.patch, cctbx-2010.03.29.2334-r2.ebuild,
+  cctbx-2010.03.29.2334-r3.ebuild:
+  Prefix boost detection fix
+
+  29 Dec 2010; Justin Lecher <jlec@g.o> cctbx-2009.11.01.0123-r1.ebuild,
+  cctbx-2010.03.29.2334-r1.ebuild, cctbx-2010.03.29.2334-r2.ebuild,
+  cctbx-2010.03.29.2334-r3.ebuild:
+  Added missing dependency on clipper
+
+  16 Dec 2010; Justin Lecher <jlec@g.o> cctbx-2009.11.01.0123-r1.ebuild,
+  cctbx-2010.03.29.2334-r1.ebuild, cctbx-2010.03.29.2334-r2.ebuild,
+  cctbx-2010.03.29.2334-r3.ebuild:
+  Added missing RDEPEND on sci-libs/clipper
+
+*cctbx-2010.03.29.2334-r3 (15 Dec 2010)
+
+  15 Dec 2010; Justin Lecher <jlec@g.o>
+  +cctbx-2010.03.29.2334-r3.ebuild:
+  Fixing all binaray wrappers
+
+  12 Sep 2010; Justin Lecher <jlec@g.o>
+  cctbx-2009.11.01.0123-r1.ebuild, cctbx-2010.03.29.2334-r1.ebuild,
+  cctbx-2010.03.29.2334-r2.ebuild:
+  Switched to tc-has-openmp and remove built_with_use
+
+*cctbx-2010.03.29.2334-r2 (12 Sep 2010)
+
+  12 Sep 2010; Justin Lecher <jlec@g.o>
+  +files/2010.03.29.2334-boost.patch, +cctbx-2010.03.29.2334-r2.ebuild,
+  +files/2010.03.29.2334-clipper.patch, +files/2010.03.29.2334-flags.patch,
+  +files/2010.03.29.2334-soname.patch:
+  Big rewrite
+
+*cctbx-2010.03.29.2334-r1 (03 Jul 2010)
+
+  03 Jul 2010; Justin Lecher <jlec@g.o>
+  +files/2010.03.29.2334-tst_server.py.patch, -cctbx-2010.03.29.2334.ebuild,
+  +cctbx-2010.03.29.2334-r1.ebuild:
+  Fix for invalid python syntax
+
+  28 Jun 2010; Christoph Mende <angelos@g.o>
+  cctbx-2010.03.29.2334.ebuild:
+  Stable on amd64 wrt bug #325965
+
+  16 Jun 2010; Justin Lecher <jlec@g.o>
+  cctbx-2009.11.01.0123-r1.ebuild, cctbx-2010.03.29.2334.ebuild:
+  Last fixes for prefix and keyworded for *-linux
+
+*cctbx-2010.03.29.2334 (22 May 2010)
+
+  22 May 2010; Justin Lecher <jlec@g.o>
+  +cctbx-2010.03.29.2334.ebuild:
+  Version bump
+
+  14 Feb 2010; Justin Lecher (jlec) <jlec@g.o>
+  -cctbx-2009.11.01.0123.ebuild, +cctbx-2009.11.01.0123-r1.ebuild:
+  Workaround for broken python.eclass
+
+*cctbx-2009.11.01.0123-r1 (13 Feb 2010)
+
+  13 Feb 2010; Justin Lecher (jlec) <jlec@g.o>
+  +cctbx-2009.11.01.0123-r1.ebuild:
+  Correct usage of new python.eclass
+
+*cctbx-2009.11.01.0123 (04 Feb 2010)
+
+  04 Feb 2010; Justin Lecher (jlec) <jlec@g.o>
+  +cctbx-2009.11.01.0123.ebuild, +metadata.xml:
+  New ebuild, initialy written by dberkholz
+

diff --git a/sci-libs/cctbx/cctbx-2012.05.08.2305.ebuild b/sci-libs/cctbx/cctbx-2012.05.08.2305.ebuild
new file mode 100644
index 0000000..ac51db7
--- /dev/null
+++ b/sci-libs/cctbx/cctbx-2012.05.08.2305.ebuild
@@ -0,0 +1,81 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/cctbx/cctbx-2010.03.29.2334-r7.ebuild,v 1.3 2013/03/19 07:07:15 jlec Exp $
+
+EAPI=5
+
+DISTUTILS_SINGLE_IMPL=true
+PYTHON_COMPAT=( python{2_6,2_7} )
+
+inherit  distutils-r1 eutils fortran-2 multilib toolchain-funcs
+
+MY_PV="${PV//./_}"
+
+DESCRIPTION="Computational Crystallography Toolbox"
+HOMEPAGE="http://cctbx.sourceforge.net/"
+SRC_URI="http://cci.lbl.gov/cctbx_build/results/${MY_PV}/${PN}_bundle.tar.gz -> ${P}.tar.gz"
+
+LICENSE="cctbx-2.0"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="+minimal"
+
+RDEPEND="
+	>=dev-libs/boost-1.48[python,${PYTHON_USEDEP}]
+	sci-libs/clipper
+	sci-libs/fftw:2.1
+	sci-libs/libccp4
+	!minimal? (
+		sci-chemistry/cns
+		sci-chemistry/shelx )"
+DEPEND="${RDEPEND}
+	!prefix? ( >=dev-util/scons-1.2[${PYTHON_USEDEP}] )"
+
+S="${WORKDIR}"
+MY_S="${WORKDIR}"/cctbx_sources
+MY_B="${WORKDIR}"/cctbx_build
+
+pkg_setup() {
+	use openmp && FORTRAN_NEED_OPENMP="1"
+	if use openmp && ! tc-has-openmp; then
+		ewarn "You are using gcc and OpenMP is only available with gcc >= 4.2 and icc"
+		ewarn "If you want to build ${PN} with OpenMP, abort now,"
+		ewarn "and switch CC to an OpenMP capable compiler"
+		FORTRAN_NEED_OPENMP=1
+	fi
+	fortran-2_pkg_setup
+	python-single-r1_pkg_setup
+}
+
+python_prepare_all() {
+	local opts
+	local optsld
+
+	EPATCH_OPTS="-p1" \
+	epatch \
+		"${FILESDIR}"/${PV}/*patch
+
+	export MULTILIBDIR=$(get_libdir)
+
+	# Clean sources
+	rm -rf "${MY_S}"/boost/* || die
+	rm -rf "${MY_S}"/PyCifRW/* || die
+	find "${MY_S}"/cbflib -maxdepth 1 -mindepth 1 -not -name examples -exec rm -rf {} + || die
+	find "${MY_S}"/ccp4io/lib -maxdepth 1 -mindepth 1 -not -name ssm -exec rm -rf {} + || die
+	find "${MY_S}"/clipper -maxdepth 1 -mindepth 1 -not -name clipper -exec rm -rf {} + || die
+#	find "${MY_S}"/clipper/clipper -maxdepth 1 -mindepth 1 \( -not -name cctbx -a -not -name contrib \) -exec rm -rf {} + || die
+	find "${MY_S}"/clipper/clipper -maxdepth 1 -mindepth 1 -not -name cctbx -exec rm -rf {} + || die
+	rm -rf "${MY_S}"/gui_resources/gl2ps || die
+#	rm -rf "${MY_S}"/scons || die
+	rm -rf "${MY_S}"/ucif/antlr3 || die
+#	rm -rvf "${MY_S}"/ccp4io/lib/ssm || die
+
+#	find "${MY_S}/clipper" -name "*.h" -print -delete >> "${T}"/clean.log || die
+
+	if ! use prefix; then
+		rm -rvf "${MY_S}/scons" >> "${T}"/clean.log || die
+		echo "import os, sys; os.execvp('scons', sys.argv)" > "${MY_S}"/libtbx/command_line/scons.py || die
+	fi
+
+	distutils-r1_python_prepare_all
+}

diff --git a/sci-libs/cctbx/cctbx-2013.02.27.0005.ebuild b/sci-libs/cctbx/cctbx-2013.02.27.0005.ebuild
new file mode 100644
index 0000000..ac51db7
--- /dev/null
+++ b/sci-libs/cctbx/cctbx-2013.02.27.0005.ebuild
@@ -0,0 +1,81 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/cctbx/cctbx-2010.03.29.2334-r7.ebuild,v 1.3 2013/03/19 07:07:15 jlec Exp $
+
+EAPI=5
+
+DISTUTILS_SINGLE_IMPL=true
+PYTHON_COMPAT=( python{2_6,2_7} )
+
+inherit  distutils-r1 eutils fortran-2 multilib toolchain-funcs
+
+MY_PV="${PV//./_}"
+
+DESCRIPTION="Computational Crystallography Toolbox"
+HOMEPAGE="http://cctbx.sourceforge.net/"
+SRC_URI="http://cci.lbl.gov/cctbx_build/results/${MY_PV}/${PN}_bundle.tar.gz -> ${P}.tar.gz"
+
+LICENSE="cctbx-2.0"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="+minimal"
+
+RDEPEND="
+	>=dev-libs/boost-1.48[python,${PYTHON_USEDEP}]
+	sci-libs/clipper
+	sci-libs/fftw:2.1
+	sci-libs/libccp4
+	!minimal? (
+		sci-chemistry/cns
+		sci-chemistry/shelx )"
+DEPEND="${RDEPEND}
+	!prefix? ( >=dev-util/scons-1.2[${PYTHON_USEDEP}] )"
+
+S="${WORKDIR}"
+MY_S="${WORKDIR}"/cctbx_sources
+MY_B="${WORKDIR}"/cctbx_build
+
+pkg_setup() {
+	use openmp && FORTRAN_NEED_OPENMP="1"
+	if use openmp && ! tc-has-openmp; then
+		ewarn "You are using gcc and OpenMP is only available with gcc >= 4.2 and icc"
+		ewarn "If you want to build ${PN} with OpenMP, abort now,"
+		ewarn "and switch CC to an OpenMP capable compiler"
+		FORTRAN_NEED_OPENMP=1
+	fi
+	fortran-2_pkg_setup
+	python-single-r1_pkg_setup
+}
+
+python_prepare_all() {
+	local opts
+	local optsld
+
+	EPATCH_OPTS="-p1" \
+	epatch \
+		"${FILESDIR}"/${PV}/*patch
+
+	export MULTILIBDIR=$(get_libdir)
+
+	# Clean sources
+	rm -rf "${MY_S}"/boost/* || die
+	rm -rf "${MY_S}"/PyCifRW/* || die
+	find "${MY_S}"/cbflib -maxdepth 1 -mindepth 1 -not -name examples -exec rm -rf {} + || die
+	find "${MY_S}"/ccp4io/lib -maxdepth 1 -mindepth 1 -not -name ssm -exec rm -rf {} + || die
+	find "${MY_S}"/clipper -maxdepth 1 -mindepth 1 -not -name clipper -exec rm -rf {} + || die
+#	find "${MY_S}"/clipper/clipper -maxdepth 1 -mindepth 1 \( -not -name cctbx -a -not -name contrib \) -exec rm -rf {} + || die
+	find "${MY_S}"/clipper/clipper -maxdepth 1 -mindepth 1 -not -name cctbx -exec rm -rf {} + || die
+	rm -rf "${MY_S}"/gui_resources/gl2ps || die
+#	rm -rf "${MY_S}"/scons || die
+	rm -rf "${MY_S}"/ucif/antlr3 || die
+#	rm -rvf "${MY_S}"/ccp4io/lib/ssm || die
+
+#	find "${MY_S}/clipper" -name "*.h" -print -delete >> "${T}"/clean.log || die
+
+	if ! use prefix; then
+		rm -rvf "${MY_S}/scons" >> "${T}"/clean.log || die
+		echo "import os, sys; os.execvp('scons', sys.argv)" > "${MY_S}"/libtbx/command_line/scons.py || die
+	fi
+
+	distutils-r1_python_prepare_all
+}

diff --git a/sci-libs/cctbx/files/2012.05.08.2305/0001-remove-hardcoded-libtbx_build-env.patch b/sci-libs/cctbx/files/2012.05.08.2305/0001-remove-hardcoded-libtbx_build-env.patch
new file mode 100644
index 0000000..14d3f09
--- /dev/null
+++ b/sci-libs/cctbx/files/2012.05.08.2305/0001-remove-hardcoded-libtbx_build-env.patch
@@ -0,0 +1,24 @@
+From: =?UTF-8?q?Picca=20Fr=C3=A9d=C3=A9ric-Emmanuel?= <picca@××××××.org>
+Date: Sat, 30 Jun 2012 15:50:22 +0200
+Subject: remove-hardcoded-libtbx_build-env
+
+---
+ cctbx_sources/libtbx/env_config.py |    5 ++++-
+ 1 file changed, 4 insertions(+), 1 deletion(-)
+
+diff --git a/cctbx_sources/libtbx/env_config.py b/cctbx_sources/libtbx/env_config.py
+index 9c01e0f..8a62446 100644
+--- a/cctbx_sources/libtbx/env_config.py
++++ b/cctbx_sources/libtbx/env_config.py
+@@ -2147,7 +2147,10 @@ def cold_start(args):
+   env.refresh()
+ 
+ def unpickle():
+-  build_path = os.environ["LIBTBX_BUILD"]
++  if os.environ.has_key("LIBTBX_BUILD"):
++    build_path = os.environ["LIBTBX_BUILD"]
++  else:
++    build_path = "/usr/share/cctbx/python%d.%d"%(sys.version_info[:2])
+   set_preferred_sys_prefix_and_sys_executable(build_path=build_path)
+   libtbx_env = open(op.join(build_path, "libtbx_env"), "rb")
+   env = pickle.load(libtbx_env)

diff --git a/sci-libs/cctbx/files/2012.05.08.2305/0002-fix-opengl-header-missing-gltbx.patch b/sci-libs/cctbx/files/2012.05.08.2305/0002-fix-opengl-header-missing-gltbx.patch
new file mode 100644
index 0000000..d3684a5
--- /dev/null
+++ b/sci-libs/cctbx/files/2012.05.08.2305/0002-fix-opengl-header-missing-gltbx.patch
@@ -0,0 +1,51 @@
+From: =?UTF-8?q?Picca=20Fr=C3=A9d=C3=A9ric-Emmanuel?= <picca@××××××.org>
+Date: Sat, 30 Jun 2012 15:51:06 +0200
+Subject: fix-opengl-header-missing-gltbx
+
+---
+ cctbx_sources/gltbx/SConscript |   32 ++++++++++++++++----------------
+ 1 file changed, 16 insertions(+), 16 deletions(-)
+
+diff --git a/cctbx_sources/gltbx/SConscript b/cctbx_sources/gltbx/SConscript
+index d02e7a5..4b2213d 100644
+--- a/cctbx_sources/gltbx/SConscript
++++ b/cctbx_sources/gltbx/SConscript
+@@ -45,22 +45,22 @@ if (not env_etc.no_boost_python):
+     env=env,
+     paths=env_etc.gltbx_common_includes + [env_etc.python_include])
+   #
+-  env_etc.gltbx_has_usable_opengl = False
+-  conf = trial_env.Configure()
+-  flag, output = conf.TryRun("""
+-#include <gltbx/include_opengl.h>
+-#include <iostream>
+-int main() { std::cout << GL_POINT << std::endl; return 0; }
+-""", extension=".cpp")
+-  conf.Finish()
+-  if (flag and len(output.strip()) != 0):
+-    conf = env.Configure()
+-    if (conf.TryCompile("""
+-#include <gltbx/include_opengl.h>
+-""", extension=".cpp")):
+-      env_etc.gltbx_has_usable_opengl = True
+-    conf.Finish()
+-  #
++  env_etc.gltbx_has_usable_opengl = True
++#  conf = trial_env.Configure()
++#  flag, output = conf.TryRun("""
++##include <gltbx/include_opengl.h>
++##include <iostream>
++#int main() { std::cout << GL_POINT << std::endl; return 0; }
++#""", extension=".cpp")
++#  conf.Finish()
++#  if (flag and len(output.strip()) != 0):
++#    conf = env.Configure()
++#    if (conf.TryCompile("""
++##include <gltbx/include_opengl.h>
++#""", extension=".cpp")):
++#      env_etc.gltbx_has_usable_opengl = True
++#    conf.Finish()
++#  #
+   if (not env_etc.gltbx_has_usable_opengl):
+     print "gltbx: OpenGL headers and/or libraries not available."
+     print "gltbx: Compilation skipped."

diff --git a/sci-libs/cctbx/files/2012.05.08.2305/0003-correct-paths-in-dispatcher-creation.patch b/sci-libs/cctbx/files/2012.05.08.2305/0003-correct-paths-in-dispatcher-creation.patch
new file mode 100644
index 0000000..4fe0ea3
--- /dev/null
+++ b/sci-libs/cctbx/files/2012.05.08.2305/0003-correct-paths-in-dispatcher-creation.patch
@@ -0,0 +1,85 @@
+From: =?UTF-8?q?Picca=20Fr=C3=A9d=C3=A9ric-Emmanuel?= <picca@××××××.org>
+Date: Sat, 30 Jun 2012 16:01:20 +0200
+Subject: correct-paths-in-dispatcher-creation
+
+---
+ cctbx_sources/libtbx/env_config.py |   48 ++++++++++++++++++------------------
+ 1 file changed, 24 insertions(+), 24 deletions(-)
+
+diff --git a/cctbx_sources/libtbx/env_config.py b/cctbx_sources/libtbx/env_config.py
+index 8a62446..c3e1c7d 100644
+--- a/cctbx_sources/libtbx/env_config.py
++++ b/cctbx_sources/libtbx/env_config.py
+@@ -894,26 +894,26 @@ Wait for the command to finish, then try again.""" % vars())
+       print >> f, '# command at the end.'
+     print >> f, '#'
+     write_do_not_edit(f=f)
+-    print >> f, '# To customize this auto-generated script create'
++    #print >> f, '# To customize this auto-generated script create'
+     print >> f, '#'
+-    print >> f, '#   dispatcher_include*.sh'
++    #print >> f, '#   dispatcher_include*.sh'
+     print >> f, '#'
+-    print >> f, '# files in %s and run' % show_string(abs(self.build_path))
++    #print >> f, '# files in %s and run' % show_string(abs(self.build_path))
+     print >> f, '#'
+-    print >> f, '#   libtbx.refresh'
++    #print >> f, '#   libtbx.refresh'
+     print >> f, '#'
+     print >> f, '# to re-generate the dispatchers (libtbx.refresh is a subset'
+     print >> f, '# of the functionality of the libtbx/configure.py command).'
+     print >> f, '#'
+-    print >> f, '# See also:'
+-    print >> f, '#   %s' \
+-      % show_string(self.under_build("dispatcher_include_template.sh"))
++    #print >> f, '# See also:'
++    #print >> f, '#   %s' \
++    #  % show_string(self.under_build("dispatcher_include_template.sh"))
+     print >> f, '#'
+     print >> f, 'unset PYTHONHOME'
+     print >> f, 'LC_ALL=C'
+     print >> f, 'export LC_ALL'
+-    print >> f, 'LIBTBX_BUILD="$(cd "$(dirname "$0")" && cd .. && pwd -P)"'
+-    print >> f, 'export LIBTBX_BUILD'
++    #print >> f, 'LIBTBX_BUILD="$(cd "$(dirname "$0")" && cd .. && pwd -P)"'
++    #print >> f, 'export LIBTBX_BUILD'
+     print >> f, 'LIBTBX_PYEXE_BASENAME="%s"' % self.python_exe.basename()
+     print >> f, 'export LIBTBX_PYEXE_BASENAME'
+     source_is_py = False
+@@ -930,21 +930,21 @@ Wait for the command to finish, then try again.""" % vars())
+         source_is_py = True
+     for line in self.dispatcher_include(where="at_start"):
+       print >> f, line
+-    essentials = [("PYTHONPATH", self.pythonpath)]
+-    essentials.append((
+-      ld_library_path_var_name(),
+-      self.ld_library_path_additions()))
+-    essentials.append(("PATH", [self.bin_path]))
+-    for n,v in essentials:
+-      if (len(v) == 0): continue
+-      v = ":".join([p.sh_value() for p in v])
+-      print >> f, 'if [ -n "$%s" ]; then' % n
+-      print >> f, '  %s="%s:$%s"' % (n, v, n)
+-      print >> f, '  export %s' % n
+-      print >> f, 'else'
+-      print >> f, '  %s="%s"' % (n, v)
+-      print >> f, '  export %s' % n
+-      print >> f, 'fi'
++    # essentials = [("PYTHONPATH", self.pythonpath)]
++    # essentials.append((
++    #   ld_library_path_var_name(),
++    #   self.ld_library_path_additions()))
++    # essentials.append(("PATH", [self.bin_path]))
++    # for n,v in essentials:
++    #   if (len(v) == 0): continue
++    #   v = ":".join([p.sh_value() for p in v])
++    #   print >> f, 'if [ -n "$%s" ]; then' % n
++    #   print >> f, '  %s="%s:$%s"' % (n, v, n)
++    #   print >> f, '  export %s' % n
++    #   print >> f, 'else'
++    #   print >> f, '  %s="%s"' % (n, v)
++    #   print >> f, '  export %s' % n
++    #   print >> f, 'fi'
+     precall_commands = self.dispatcher_precall_commands()
+     if (precall_commands is not None):
+       for line in precall_commands:

diff --git a/sci-libs/cctbx/files/2012.05.08.2305/0004-upstream-fix-for-declaration-errors-in-gcc4.7.patch b/sci-libs/cctbx/files/2012.05.08.2305/0004-upstream-fix-for-declaration-errors-in-gcc4.7.patch
new file mode 100644
index 0000000..a3acee5
--- /dev/null
+++ b/sci-libs/cctbx/files/2012.05.08.2305/0004-upstream-fix-for-declaration-errors-in-gcc4.7.patch
@@ -0,0 +1,442 @@
+From: Radostan Riedel <raybuntu@××××××××××.com>
+Date: Mon, 9 Jul 2012 19:37:49 +0200
+Subject: upstream fix for declaration errors in gcc4.7
+
+---
+ cctbx_sources/mmtbx/bulk_solvent/bulk_solvent.h |  416 +++++++++++------------
+ 1 file changed, 208 insertions(+), 208 deletions(-)
+
+diff --git a/cctbx_sources/mmtbx/bulk_solvent/bulk_solvent.h b/cctbx_sources/mmtbx/bulk_solvent/bulk_solvent.h
+index 6959f18..0be075f 100644
+--- a/cctbx_sources/mmtbx/bulk_solvent/bulk_solvent.h
++++ b/cctbx_sources/mmtbx/bulk_solvent/bulk_solvent.h
+@@ -322,6 +322,214 @@ private:
+ };
+ 
+ //------------------------------------------------------------------------------
++template <typename FloatType, typename ComplexType>
++FloatType
++scale(af::const_ref<FloatType> const& fo,
++      af::const_ref<ComplexType> const& fc)
++{
++    MMTBX_ASSERT(fo.size()==fc.size());
++    FloatType num=0.0;
++    FloatType denum=0.0;
++    for(std::size_t i=0; i < fo.size(); i++) {
++      FloatType fc_abs = std::abs(fc[i]);
++      num += fo[i] * fc_abs;
++      denum += fc_abs * fc_abs;
++    }
++    return (denum == 0 ? 0 : num/denum);
++};
++
++template <typename FloatType, typename ComplexType>
++FloatType
++scale(af::const_ref<FloatType> const& fo,
++      af::const_ref<ComplexType> const& fc,
++      af::const_ref<bool> const& selection)
++{
++    MMTBX_ASSERT(fo.size()==fc.size());
++    MMTBX_ASSERT(fo.size()==selection.size());
++    FloatType num=0.0;
++    FloatType denum=0.0;
++    for(std::size_t i=0; i < fo.size(); i++) {
++      if(selection[i]) {
++        FloatType fc_abs = std::abs(fc[i]);
++        num += fo[i] * fc_abs;
++        denum += fc_abs * fc_abs;
++      }
++    }
++    return (denum == 0 ? 0 : num/denum);
++};
++
++
++template <typename FloatType>
++FloatType
++scale(af::const_ref<FloatType> const& fo,
++      af::const_ref<FloatType> const& fc)
++{
++    MMTBX_ASSERT(fo.size()==fc.size());
++    FloatType num=0.0;
++    FloatType denum=0.0;
++    for(std::size_t i=0; i < fo.size(); i++) {
++      num += fo[i] * fc[i];
++      denum += fc[i] * fc[i];
++    }
++    return (denum == 0 ? 0 : num/denum);
++};
++
++template <typename FloatType, typename ComplexType>
++FloatType
++scale(
++  af::const_ref<FloatType> const& fo,
++  af::const_ref< std::complex<ComplexType> > const& fc1,
++  af::const_ref< std::complex<ComplexType> > const& fc2,
++  FloatType const& twin_fraction)
++{
++  MMTBX_ASSERT(fo.size()==fc1.size());
++  MMTBX_ASSERT(fo.size()==fc2.size());
++  af::shared<FloatType> fc_abs(fo.size());
++  for(std::size_t i=0; i < fo.size(); i++) {
++    FloatType fc_abs1 = std::abs(fc1[i]);
++    FloatType fc_abs2 = std::abs(fc2[i]);
++    fc_abs[i]=std::sqrt((1-twin_fraction)*fc_abs1*fc_abs1+
++                           twin_fraction *fc_abs2*fc_abs2);
++  }
++  return scale(fo,fc_abs.const_ref());
++};
++
++template <typename FloatType>
++FloatType
++r_factor(
++  af::const_ref<FloatType> const& fo,
++  af::const_ref<FloatType> const& fc,
++  FloatType const& scale)
++{
++  MMTBX_ASSERT(fo.size()==fc.size());
++  FloatType num=0.0;
++  FloatType denum=0.0;
++  for(std::size_t i=0; i < fo.size(); i++) {
++    num += std::abs(fo[i] - fc[i] * scale);
++    denum += fo[i];
++  }
++  if(denum == 0) return 1.e+9;
++  return num/denum;
++};
++
++template <typename FloatType>
++FloatType
++r_factor(
++  af::const_ref<FloatType> const& fo,
++  af::const_ref< std::complex<FloatType> > const& fc,
++  FloatType const& scale)
++{
++  MMTBX_ASSERT(fo.size()==fc.size());
++  FloatType num=0.0;
++  FloatType denum=0.0;
++  for(std::size_t i=0; i < fo.size(); i++) {
++    num += std::abs(fo[i] - std::abs(fc[i]) * scale);
++    denum += fo[i];
++  }
++  if(denum == 0) return 1.e+9;
++  return num/denum;
++};
++
++template <typename FloatType>
++FloatType
++r_factor(
++  af::const_ref<FloatType> const& fo,
++  af::const_ref< std::complex<FloatType> > const& fc,
++  af::const_ref<bool> const& selection,
++  FloatType const& scale)
++{
++  MMTBX_ASSERT(fo.size()==fc.size());
++  MMTBX_ASSERT(fo.size()==selection.size());
++  FloatType num=0.0;
++  FloatType denum=0.0;
++  for(std::size_t i=0; i < fo.size(); i++) {
++    if(selection[i]) {
++      num += std::abs(fo[i] - std::abs(fc[i]) * scale);
++      denum += fo[i];
++    }
++  }
++  if(denum == 0) return 1.e+9;
++  return num/denum;
++};
++
++template <typename FloatType>
++FloatType
++r_factor(
++  af::const_ref<FloatType> const& fo,
++  af::const_ref<FloatType> const& fc)
++{
++  MMTBX_ASSERT(fo.size()==fc.size());
++  FloatType sc = scale(fo,fc);
++  return r_factor(fo,fc,sc);
++};
++
++template <typename FloatType, typename ComplexType>
++FloatType
++r_factor(
++  af::const_ref<FloatType> const& fo,
++  af::const_ref<std::complex<ComplexType> > const& fc)
++{
++  MMTBX_ASSERT(fo.size()==fc.size());
++  FloatType sc = scale(fo,fc);
++  return r_factor(fo,fc,sc);
++};
++
++template <typename FloatType, typename ComplexType>
++FloatType
++r_factor(
++  af::const_ref<FloatType> const& fo,
++  af::const_ref<std::complex<ComplexType> > const& fc,
++  af::const_ref<bool> const& selection)
++{
++  MMTBX_ASSERT(fo.size()==fc.size());
++  MMTBX_ASSERT(fo.size()==selection.size());
++  FloatType sc = scale(fo,fc,selection);
++  return r_factor(fo,fc,selection,sc);
++};
++
++template <typename FloatType, typename ComplexType>
++FloatType
++r_factor(
++  af::const_ref<FloatType> const& fo,
++  af::const_ref< std::complex<ComplexType> > const& fc1,
++  af::const_ref< std::complex<ComplexType> > const& fc2,
++  FloatType const& twin_fraction)
++{
++  MMTBX_ASSERT(fo.size()==fc1.size());
++  MMTBX_ASSERT(fo.size()==fc2.size());
++  af::shared<FloatType> fc_abs(fo.size());
++  for(std::size_t i=0; i < fo.size(); i++) {
++    FloatType fc_abs1 = std::abs(fc1[i]);
++    FloatType fc_abs2 = std::abs(fc2[i]);
++    fc_abs[i]=std::sqrt((1-twin_fraction)*fc_abs1*fc_abs1+
++                           twin_fraction *fc_abs2*fc_abs2);
++  }
++  FloatType sc = scale(fo,fc_abs.const_ref());
++  return r_factor(fo,fc_abs.const_ref(),sc);
++};
++
++template <typename FloatType, typename ComplexType>
++FloatType
++r_factor(
++  af::const_ref<FloatType> const& fo,
++  af::const_ref< std::complex<ComplexType> > const& fc1,
++  af::const_ref< std::complex<ComplexType> > const& fc2,
++  FloatType const& twin_fraction,
++  FloatType const& scale)
++{
++  MMTBX_ASSERT(fo.size()==fc1.size());
++  MMTBX_ASSERT(fo.size()==fc2.size());
++  af::shared<FloatType> fc_abs(fo.size());
++  for(std::size_t i=0; i < fo.size(); i++) {
++    FloatType fc_abs1 = std::abs(fc1[i]);
++    FloatType fc_abs2 = std::abs(fc2[i]);
++    fc_abs[i]=std::sqrt((1-twin_fraction)*fc_abs1*fc_abs1+
++                           twin_fraction *fc_abs2*fc_abs2);
++  }
++  return r_factor(fo,fc_abs.const_ref(),scale);
++};
++
++//------------------------------------------------------------------------------
+ // All scales (overall, overall anisotropic, etc) must be applied.
+ template <
+   typename FloatType=double,
+@@ -744,214 +952,6 @@ template <typename FloatType>
+  };
+ 
+ //------------------------------------------------------------------------------
+-template <typename FloatType, typename ComplexType>
+-FloatType
+-scale(af::const_ref<FloatType> const& fo,
+-      af::const_ref<ComplexType> const& fc)
+-{
+-    MMTBX_ASSERT(fo.size()==fc.size());
+-    FloatType num=0.0;
+-    FloatType denum=0.0;
+-    for(std::size_t i=0; i < fo.size(); i++) {
+-      FloatType fc_abs = std::abs(fc[i]);
+-      num += fo[i] * fc_abs;
+-      denum += fc_abs * fc_abs;
+-    }
+-    return (denum == 0 ? 0 : num/denum);
+-};
+-
+-template <typename FloatType, typename ComplexType>
+-FloatType
+-scale(af::const_ref<FloatType> const& fo,
+-      af::const_ref<ComplexType> const& fc,
+-      af::const_ref<bool> const& selection)
+-{
+-    MMTBX_ASSERT(fo.size()==fc.size());
+-    MMTBX_ASSERT(fo.size()==selection.size());
+-    FloatType num=0.0;
+-    FloatType denum=0.0;
+-    for(std::size_t i=0; i < fo.size(); i++) {
+-      if(selection[i]) {
+-        FloatType fc_abs = std::abs(fc[i]);
+-        num += fo[i] * fc_abs;
+-        denum += fc_abs * fc_abs;
+-      }
+-    }
+-    return (denum == 0 ? 0 : num/denum);
+-};
+-
+-
+-template <typename FloatType>
+-FloatType
+-scale(af::const_ref<FloatType> const& fo,
+-      af::const_ref<FloatType> const& fc)
+-{
+-    MMTBX_ASSERT(fo.size()==fc.size());
+-    FloatType num=0.0;
+-    FloatType denum=0.0;
+-    for(std::size_t i=0; i < fo.size(); i++) {
+-      num += fo[i] * fc[i];
+-      denum += fc[i] * fc[i];
+-    }
+-    return (denum == 0 ? 0 : num/denum);
+-};
+-
+-template <typename FloatType, typename ComplexType>
+-FloatType
+-scale(
+-  af::const_ref<FloatType> const& fo,
+-  af::const_ref< std::complex<ComplexType> > const& fc1,
+-  af::const_ref< std::complex<ComplexType> > const& fc2,
+-  FloatType const& twin_fraction)
+-{
+-  MMTBX_ASSERT(fo.size()==fc1.size());
+-  MMTBX_ASSERT(fo.size()==fc2.size());
+-  af::shared<FloatType> fc_abs(fo.size());
+-  for(std::size_t i=0; i < fo.size(); i++) {
+-    FloatType fc_abs1 = std::abs(fc1[i]);
+-    FloatType fc_abs2 = std::abs(fc2[i]);
+-    fc_abs[i]=std::sqrt((1-twin_fraction)*fc_abs1*fc_abs1+
+-                           twin_fraction *fc_abs2*fc_abs2);
+-  }
+-  return scale(fo,fc_abs.const_ref());
+-};
+-
+-template <typename FloatType>
+-FloatType
+-r_factor(
+-  af::const_ref<FloatType> const& fo,
+-  af::const_ref<FloatType> const& fc,
+-  FloatType const& scale)
+-{
+-  MMTBX_ASSERT(fo.size()==fc.size());
+-  FloatType num=0.0;
+-  FloatType denum=0.0;
+-  for(std::size_t i=0; i < fo.size(); i++) {
+-    num += std::abs(fo[i] - fc[i] * scale);
+-    denum += fo[i];
+-  }
+-  if(denum == 0) return 1.e+9;
+-  return num/denum;
+-};
+-
+-template <typename FloatType>
+-FloatType
+-r_factor(
+-  af::const_ref<FloatType> const& fo,
+-  af::const_ref< std::complex<FloatType> > const& fc,
+-  FloatType const& scale)
+-{
+-  MMTBX_ASSERT(fo.size()==fc.size());
+-  FloatType num=0.0;
+-  FloatType denum=0.0;
+-  for(std::size_t i=0; i < fo.size(); i++) {
+-    num += std::abs(fo[i] - std::abs(fc[i]) * scale);
+-    denum += fo[i];
+-  }
+-  if(denum == 0) return 1.e+9;
+-  return num/denum;
+-};
+-
+-template <typename FloatType>
+-FloatType
+-r_factor(
+-  af::const_ref<FloatType> const& fo,
+-  af::const_ref< std::complex<FloatType> > const& fc,
+-  af::const_ref<bool> const& selection,
+-  FloatType const& scale)
+-{
+-  MMTBX_ASSERT(fo.size()==fc.size());
+-  MMTBX_ASSERT(fo.size()==selection.size());
+-  FloatType num=0.0;
+-  FloatType denum=0.0;
+-  for(std::size_t i=0; i < fo.size(); i++) {
+-    if(selection[i]) {
+-      num += std::abs(fo[i] - std::abs(fc[i]) * scale);
+-      denum += fo[i];
+-    }
+-  }
+-  if(denum == 0) return 1.e+9;
+-  return num/denum;
+-};
+-
+-template <typename FloatType>
+-FloatType
+-r_factor(
+-  af::const_ref<FloatType> const& fo,
+-  af::const_ref<FloatType> const& fc)
+-{
+-  MMTBX_ASSERT(fo.size()==fc.size());
+-  FloatType sc = scale(fo,fc);
+-  return r_factor(fo,fc,sc);
+-};
+-
+-template <typename FloatType, typename ComplexType>
+-FloatType
+-r_factor(
+-  af::const_ref<FloatType> const& fo,
+-  af::const_ref<std::complex<ComplexType> > const& fc)
+-{
+-  MMTBX_ASSERT(fo.size()==fc.size());
+-  FloatType sc = scale(fo,fc);
+-  return r_factor(fo,fc,sc);
+-};
+-
+-template <typename FloatType, typename ComplexType>
+-FloatType
+-r_factor(
+-  af::const_ref<FloatType> const& fo,
+-  af::const_ref<std::complex<ComplexType> > const& fc,
+-  af::const_ref<bool> const& selection)
+-{
+-  MMTBX_ASSERT(fo.size()==fc.size());
+-  MMTBX_ASSERT(fo.size()==selection.size());
+-  FloatType sc = scale(fo,fc,selection);
+-  return r_factor(fo,fc,selection,sc);
+-};
+-
+-template <typename FloatType, typename ComplexType>
+-FloatType
+-r_factor(
+-  af::const_ref<FloatType> const& fo,
+-  af::const_ref< std::complex<ComplexType> > const& fc1,
+-  af::const_ref< std::complex<ComplexType> > const& fc2,
+-  FloatType const& twin_fraction)
+-{
+-  MMTBX_ASSERT(fo.size()==fc1.size());
+-  MMTBX_ASSERT(fo.size()==fc2.size());
+-  af::shared<FloatType> fc_abs(fo.size());
+-  for(std::size_t i=0; i < fo.size(); i++) {
+-    FloatType fc_abs1 = std::abs(fc1[i]);
+-    FloatType fc_abs2 = std::abs(fc2[i]);
+-    fc_abs[i]=std::sqrt((1-twin_fraction)*fc_abs1*fc_abs1+
+-                           twin_fraction *fc_abs2*fc_abs2);
+-  }
+-  FloatType sc = scale(fo,fc_abs.const_ref());
+-  return r_factor(fo,fc_abs.const_ref(),sc);
+-};
+-
+-template <typename FloatType, typename ComplexType>
+-FloatType
+-r_factor(
+-  af::const_ref<FloatType> const& fo,
+-  af::const_ref< std::complex<ComplexType> > const& fc1,
+-  af::const_ref< std::complex<ComplexType> > const& fc2,
+-  FloatType const& twin_fraction,
+-  FloatType const& scale)
+-{
+-  MMTBX_ASSERT(fo.size()==fc1.size());
+-  MMTBX_ASSERT(fo.size()==fc2.size());
+-  af::shared<FloatType> fc_abs(fo.size());
+-  for(std::size_t i=0; i < fo.size(); i++) {
+-    FloatType fc_abs1 = std::abs(fc1[i]);
+-    FloatType fc_abs2 = std::abs(fc2[i]);
+-    fc_abs[i]=std::sqrt((1-twin_fraction)*fc_abs1*fc_abs1+
+-                           twin_fraction *fc_abs2*fc_abs2);
+-  }
+-  return r_factor(fo,fc_abs.const_ref(),scale);
+-};
+-
+-//------------------------------------------------------------------------------
+ 
+ template <typename DataType, typename TagType>
+ void

diff --git a/sci-libs/cctbx/files/2012.05.08.2305/0005-fix-for-gcc4.7-compilation-error.patch b/sci-libs/cctbx/files/2012.05.08.2305/0005-fix-for-gcc4.7-compilation-error.patch
new file mode 100644
index 0000000..f2b9523
--- /dev/null
+++ b/sci-libs/cctbx/files/2012.05.08.2305/0005-fix-for-gcc4.7-compilation-error.patch
@@ -0,0 +1,83 @@
+From: Radostan Riedel <raybuntu@××××××××××.com>
+Date: Mon, 9 Jul 2012 19:58:46 +0200
+Subject: fix for gcc4.7 compilation error
+
+---
+ .../scitbx/math/boost_python/distributions.cpp     |   60 +++++++++++++-------
+ 1 file changed, 41 insertions(+), 19 deletions(-)
+
+diff --git a/cctbx_sources/scitbx/math/boost_python/distributions.cpp b/cctbx_sources/scitbx/math/boost_python/distributions.cpp
+index e430cad..3d16a9c 100644
+--- a/cctbx_sources/scitbx/math/boost_python/distributions.cpp
++++ b/cctbx_sources/scitbx/math/boost_python/distributions.cpp
+@@ -75,29 +75,51 @@ namespace {
+   {
+     typedef Distribution wt;
+ 
++    #define NEW_MEMBER(name)                \
++    static FloatType name(wt const &self) { \
++      return boost::math::name(self);                    \
++    }
++
++    NEW_MEMBER(mean);
++    NEW_MEMBER(median);
++    NEW_MEMBER(mode);
++    NEW_MEMBER(variance);
++    NEW_MEMBER(standard_deviation);
++    NEW_MEMBER(skewness);
++    NEW_MEMBER(kurtosis);
++
++    #undef NEW_MEMBER
++
++    #define NEW_MEMBER(name)                               \
++    static FloatType name(wt const &self, FloatType arg) { \
++      return boost::math::name(self, arg);                              \
++    }
++
++    NEW_MEMBER(pdf);
++    NEW_MEMBER(cdf);
++    NEW_MEMBER(quantile);
++
++    #undef NEW_MEMBER
++
++    static scitbx::af::shared<FloatType> quantiles(wt const &self, std::size_t n) {
++      return scitbx::math::quantiles<FloatType>(self, n);
++    }
++
+     static void
+     wrap()
+     {
+       using namespace boost::python;
+-      def("mean", (FloatType(*)(wt const&)) boost::math::mean);
+-      def("median", (FloatType(*)(wt const&)) boost::math::median);
+-      def("mode", (FloatType(*)(wt const&)) boost::math::mode);
+-      def("variance", (FloatType(*)(wt const&)) boost::math::variance);
+-      def("standard_deviation",
+-        (FloatType(*)(wt const&)) boost::math::standard_deviation);
+-      def("skewness", (FloatType(*)(wt const&)) boost::math::skewness);
+-      def("kurtosis", (FloatType(*)(wt const&)) boost::math::kurtosis);
+-      def("pdf", (FloatType(*)(wt const&, FloatType const&)) boost::math::pdf);
+-      def("cdf", (FloatType(*)(wt const&, FloatType const&)) boost::math::cdf);
+-      def("quantile", (FloatType(*)(wt const&, FloatType const&))
+-        boost::math::quantile);
+-      def("quantiles",
+-#if BOOST_WORKAROUND(__EDG_VERSION__, BOOST_TESTED_AT(306))
+-        (scitbx::af::shared<FloatType>(*)(wt const&, std::size_t)) quantiles
+-#else
+-        quantiles<FloatType, wt>
+-#endif
+-        );
++      def("mean"              , mean);
++      def("median"            , median);
++      def("mode"              , mode);
++      def("variance"          , variance);
++      def("standard_deviation", standard_deviation);
++      def("skewness"          , skewness);
++      def("kurtosis"          , kurtosis);
++      def("pdf"               , pdf);
++      def("cdf"               , cdf);
++      def("quantile"          , quantile);
++      def("quantiles"         , quantiles);
+     }
+   };
+ 

diff --git a/sci-libs/cctbx/files/2012.05.08.2305/0006-options-for-system-libs-installtarget-and-prefix.patch b/sci-libs/cctbx/files/2012.05.08.2305/0006-options-for-system-libs-installtarget-and-prefix.patch
new file mode 100644
index 0000000..a3a6dd8
--- /dev/null
+++ b/sci-libs/cctbx/files/2012.05.08.2305/0006-options-for-system-libs-installtarget-and-prefix.patch
@@ -0,0 +1,1080 @@
+From: Radostan Riedel <raybuntu@××××××××××.com>
+Date: Mon, 23 Jul 2012 18:28:04 +0200
+Subject: options for system libs installtarget and prefix
+
+---
+ cctbx_sources/boost_adaptbx/SConscript             |   26 +-
+ cctbx_sources/cbflib_adaptbx/SConscript            |   89 +++---
+ .../detectors/boost_python/SConscript              |    4 +-
+ cctbx_sources/ccp4io_adaptbx/SConscript            |  284 ++++++++++----------
+ cctbx_sources/cctbx/SConscript                     |    2 +-
+ cctbx_sources/clipper_adaptbx/SConscript           |   94 ++++---
+ cctbx_sources/clipper_adaptbx/clipper/SConscript   |   10 +-
+ cctbx_sources/gltbx/SConscript                     |   20 +-
+ cctbx_sources/iotbx/cif/boost_python/SConscript    |   13 +-
+ cctbx_sources/iotbx/mtz/SConscript                 |    3 +-
+ cctbx_sources/iotbx/pdb/SConscript                 |    2 +-
+ cctbx_sources/libtbx/SConscript                    |   86 +++++-
+ cctbx_sources/libtbx/env_config.py                 |   34 +++
+ cctbx_sources/mmtbx/den/SConscript                 |    2 +-
+ cctbx_sources/mmtbx/geometry_restraints/SConscript |    2 +-
+ cctbx_sources/mmtbx/secondary_structure/SConscript |    2 +-
+ cctbx_sources/rstbx/SConscript                     |    2 +-
+ cctbx_sources/scitbx/SConscript                    |    2 +-
+ cctbx_sources/scitbx/boost_python/SConscript       |    4 +-
+ .../smtbx/refinement/boost_python/SConscript       |    4 +-
+ .../refinement/constraints/boost_python/SConscript |    4 +-
+ cctbx_sources/spotfinder/SConscript                |    2 +-
+ 22 files changed, 431 insertions(+), 260 deletions(-)
+
+diff --git a/cctbx_sources/boost_adaptbx/SConscript b/cctbx_sources/boost_adaptbx/SConscript
+index 866b1c1..68cac89 100644
+--- a/cctbx_sources/boost_adaptbx/SConscript
++++ b/cctbx_sources/boost_adaptbx/SConscript
+@@ -9,7 +9,13 @@ import sys, os
+ op = os.path
+ Import("env_base", "env_etc")
+ env_etc.boost_dist = libtbx.env.dist_path("boost")
+-env_etc.boost_include = env_etc.boost_dist
++if not env_etc.check_syslib(env_etc.boost_python, extra_libs=env_etc.py_lib)\
++    or not env_etc.check_syslib('boost_thread'):
++  env_etc.boost_include = env_etc.boost_dist
++else:
++  # This way the compiler looks in the standard location for includes
++  # should work on all platforms.
++  env_etc.boost_include = ''
+ env_etc.boost_adaptbx_dist = libtbx.env.dist_path("boost_adaptbx")
+ env_etc.boost_adaptbx_include = os.path.dirname(env_etc.boost_adaptbx_dist)
+ 
+@@ -35,9 +41,10 @@ def build_boost_thread():
+                    lo="boost/libs/thread/src/libboost_thread.lo",
+                    dylib="lib/libboost_thread.dylib")
+   env.Repository(os.path.dirname(env_etc.boost_dist))
+-  env.SharedLibrary(
+-    target='#lib/boost_thread',
+-    source=source)
++  if not env_etc.check_syslib('boost_thread'):
++    env.SharedLibrary(
++      target='#lib/boost_thread',
++      source=source)
+ 
+ build_boost_thread()
+ 
+@@ -50,7 +57,7 @@ if (not env_etc.no_boost_python):
+   env_no_includes_boost_python_ext = env_base.Clone(
+     SHLINKFLAGS=env_etc.shlinkflags_bpl,
+     SHLIBPREFIX="",
+-    LIBS=["boost_python"] + env_etc.libs_python + env_etc.libm)
++    LIBS=[env_etc.boost_python] + env_etc.libs_python + env_etc.libm)
+   env_no_includes_boost_python_ext.Append(
+     LIBPATH=env_etc.libpath_python)
+   env_no_includes_boost_python_ext.Append(
+@@ -235,10 +242,11 @@ object/function_doc_signature.cpp
+   bpl_dll_sources = [os.path.join(prefix, path) for path in bpl_dll_sources]
+   #
+   env.Repository(os.path.dirname(env_etc.boost_dist))
+-  if (env_etc.static_bpl):
+-    env.StaticLibrary(target="#lib/boost_python", source=bpl_dll_sources)
+-  else:
+-    env.SharedLibrary(target="#lib/boost_python", source=bpl_dll_sources)
++  if not env_etc.check_syslib(env_etc.boost_python, extra_libs=env_etc.py_lib):
++    if (env_etc.static_bpl):
++      env.StaticLibrary(target="#lib/boost_python", source=bpl_dll_sources)
++    else:
++      env.SharedLibrary(target="#lib/boost_python", source=bpl_dll_sources)
+   if (bool(int(ARGUMENTS.get("boost_python_tests", "0")))):
+     warn_if_unexpected_md5_hexdigest(
+       path=libtbx.env.under_dist("boost", "libs/python/test/Jamfile.v2"),
+diff --git a/cctbx_sources/cbflib_adaptbx/SConscript b/cctbx_sources/cbflib_adaptbx/SConscript
+index 4ac6717..334cfc2 100644
+--- a/cctbx_sources/cbflib_adaptbx/SConscript
++++ b/cctbx_sources/cbflib_adaptbx/SConscript
+@@ -3,9 +3,14 @@ import os
+ Import("env_base","env_etc")
+ 
+ env_etc.cbflib_dist = libtbx.env.dist_path("cbflib")
+-env_etc.cbflib_include = [env_etc.norm_join(env_etc.cbflib_dist,"examples"),
+-                          env_etc.norm_join(env_etc.cbflib_dist,"include"),
+-                          ]
++if not env_etc.check_syslib('cbf'):
++  env_etc.cbflib_include = [env_etc.norm_join(env_etc.cbflib_dist,"examples"),
++                            env_etc.norm_join(env_etc.cbflib_dist,"include"),
++                            ]
++else:
++  env_etc.cbflib_include = [env_etc.norm_join(env_etc.cbflib_dist,"examples"),
++                            "",
++                            ]
+ env_etc.cbflib_adaptbx_dist = libtbx.env.dist_path("cbflib_adaptbx")
+ 
+ env_etc.cbflib_common_includes = [
+@@ -34,39 +39,47 @@ cbflib_092_forward = []
+ if os.path.isfile( os.path.join(env_etc.cbflib_dist,"src","cbf_ws.c") ):
+   cbflib_092_forward.append("src/cbf_ws.c")
+ 
+-env.StaticLibrary(target='#lib/cbf',
+-  source = [prefix+"/"+s for s in [
+-    "examples/img.c",
+-    "src/cbf.c",
+-    "src/cbf_alloc.c",
+-    "src/cbf_ascii.c",
+-    "src/cbf_binary.c",
+-    "src/cbf_byte_offset.c",
+-    "src/cbf_canonical.c",
+-    "src/cbf_codes.c",
+-    "src/cbf_compress.c",
+-    "src/cbf_context.c",
+-    "src/cbf_file.c",
+-    "src/cbf_lex.c",
+-    "src/cbf_packed.c",
+-    "src/cbf_predictor.c",
+-    "src/cbf_read_binary.c",
+-    "src/cbf_read_mime.c",
+-    "src/cbf_simple.c",
+-    "src/cbf_string.c",
+-    "src/cbf_stx.c",
+-    "src/cbf_tree.c",
+-    "src/cbf_uncompressed.c",
+-    "src/cbf_write.c",
+-    "src/cbf_write_binary.c",
+-    "src/md5c.c",
+-  ] + cbflib_092_forward ] + [
+-    "detectors/mar_adaptor.cpp",
+-    "detectors/cbf_adaptor.cpp",
+-    "detectors/cbf_byte_offset_optimized.cpp",
+-    "detectors/buffer_based_service.cpp",
+-  ],
+-  CPPPATH=env_etc.cbflib_common_includes )
++cbflib_src = ["src/cbf.c",
++              "src/cbf_alloc.c",
++              "src/cbf_ascii.c",
++              "src/cbf_binary.c",
++              "src/cbf_byte_offset.c",
++              "src/cbf_canonical.c",
++              "src/cbf_codes.c",
++              "src/cbf_compress.c",
++              "src/cbf_context.c",
++              "src/cbf_file.c",
++              "src/cbf_lex.c",
++              "src/cbf_packed.c",
++              "src/cbf_predictor.c",
++              "src/cbf_read_binary.c",
++              "src/cbf_read_mime.c",
++              "src/cbf_simple.c",
++              "src/cbf_string.c",
++              "src/cbf_stx.c",
++              "src/cbf_tree.c",
++              "src/cbf_uncompressed.c",
++              "src/cbf_write.c",
++              "src/cbf_write_binary.c",
++              "src/md5c.c",
++             ]
++adaptor_src = ["detectors/mar_adaptor.cpp",
++               "detectors/cbf_adaptor.cpp",
++               "detectors/cbf_byte_offset_optimized.cpp",
++               "detectors/buffer_based_service.cpp",
++              ]
++if not env_etc.check_syslib('cbf'):
++  env.StaticLibrary(target='#lib/cbf',
++    source = [prefix+"/"+s for s in [
++      "examples/img.c"] + cbflib_src + cbflib_092_forward] + adaptor_src,
++    CPPPATH=env_etc.cbflib_common_includes )
++  env_etc.cbf_lib = ['cbf',]
++else:
++  env.StaticLibrary(target='#lib/cbf_adaptor',
++    source = [prefix+"/"+s for s in [
++      "examples/img.c"]] + adaptor_src,
++    CPPPATH=env_etc.cbflib_common_includes )
++  env_etc.cbf_lib = ['cbf','cbf_adaptor']
+ 
+ if (not env_etc.no_boost_python):
+   Import("env_no_includes_boost_python_ext")
+@@ -80,7 +93,7 @@ if (not env_etc.no_boost_python):
+   env_cbflib_boost_python_ext.SharedLibrary(
+     target='#lib/_pycbf',
+     source=[prefix+"/pycbf/pycbf_wrap.c"],
+-    LIBS=["cbf"]+env_etc.libs_python+env_etc.libm)
++    LIBS=env_etc.cbf_lib+env_etc.libs_python+env_etc.libm)
+ 
+   Export("env_cbflib_boost_python_ext")
+ 
+@@ -89,7 +102,7 @@ if (not env_etc.no_boost_python):
+ env_standalone = env.Clone(
+   LIBS = [env_etc.libm,],CPPPATH=env_etc.cbflib_common_includes
+ )
+-env_standalone.Prepend(LIBS=["cbf",])
++env_standalone.Prepend(LIBS=env_etc.cbf_lib)
+ 
+ for source in ["detectors/tst_memory",]:
+   target = "cbflib."+os.path.basename(source)
+diff --git a/cctbx_sources/cbflib_adaptbx/detectors/boost_python/SConscript b/cctbx_sources/cbflib_adaptbx/detectors/boost_python/SConscript
+index 2027439..8e987cc 100644
+--- a/cctbx_sources/cbflib_adaptbx/detectors/boost_python/SConscript
++++ b/cctbx_sources/cbflib_adaptbx/detectors/boost_python/SConscript
+@@ -1,6 +1,6 @@
+-Import("env_cbflib_boost_python_ext")
++Import("env_cbflib_boost_python_ext", "env_etc")
+ env = env_cbflib_boost_python_ext.Clone()
+-env.Prepend(LIBS=["cbf",])
++env.Prepend(LIBS=env_etc.cbf_lib)
+ env.SharedLibrary(
+   target="#lib/cbflib_ext",
+   source=["cbflib_ext.cpp",])
+diff --git a/cctbx_sources/ccp4io_adaptbx/SConscript b/cctbx_sources/ccp4io_adaptbx/SConscript
+index f55cc92..01600d6 100644
+--- a/cctbx_sources/ccp4io_adaptbx/SConscript
++++ b/cctbx_sources/ccp4io_adaptbx/SConscript
+@@ -36,118 +36,152 @@ else:
+   # clean out after completely removing support for
+   # old CCP4 directory structure above
+ 
+-build_ccp4io_adaptbx = libtbx.env.under_build("ccp4io_adaptbx")
+-if (not op.isdir(build_ccp4io_adaptbx)):
+-  os.mkdir(build_ccp4io_adaptbx)
+-  assert op.isdir(build_ccp4io_adaptbx)
+-
+-def replace_printf(file_name):
+-  full_path = op.join(path_lib_src, file_name)
+-  if (not op.isfile(full_path)):
+-    full_path = op.join(op.dirname(path_lib_src), "fortran", file_name)
+-  result = ["#include <ccp4io_adaptbx/printf_wrappers.h>"]
+-  for line in open(full_path).read().splitlines():
+-    for key in ["printf", "fprintf"]:
+-      matches = list(re.finditer(
+-        pattern="[^A-Za-z0-9_]%s[^A-Za-z0-9_]" % key, string=line))
+-      if (len(matches) != 0):
+-        for m in reversed(matches):
+-          s,e = m.start(), m.end()
+-          line = line[:s] \
+-               + line[s:e].replace(key, "ccp4io_%s" % key) \
+-               + line[e:]
+-    result.append(line)
+-  return "\n".join(result)
+-
+-env = env_base.Clone(
+-  SHLINKFLAGS=env_etc.shlinkflags)
+-env.Append(CCFLAGS=env_etc.ccp4io_defines)
+-env.Append(SHCCFLAGS=env_etc.ccp4io_defines)
+-env_etc.include_registry.append(
+-  env=env,
+-  paths=[
+-    "#",
+-    op.dirname(env_etc.ccp4io_include),
+-    env_etc.ccp4io_include,
+-    op.join(env_etc.ccp4io_dist, "lib", mmdb_src),
+-    op.join(env_etc.ccp4io_dist, "lib", mmdb_src, "mmdb")])
+-env.Append(LIBS=env_etc.libm)
+-if (   op.normcase(op.dirname(env_etc.ccp4io_dist))
+-    != op.normcase("ccp4io")):
+-  env.Repository(op.dirname(env_etc.ccp4io_dist))
+ source = []
+-
+ c_files = []
+-c_files.extend(["%s/%s" % (ccp4_src, bn ) for bn in """\
+-library_err.c
+-library_file.c
+-library_utils.c
+-ccp4_array.c
+-ccp4_parser.c
+-ccp4_unitcell.c
+-cvecmat.c
+-cmtzlib.c
+-""".splitlines()])
+-open(op.join(build_ccp4io_adaptbx, "csymlib.c"), "w").write(
+-  open(op.join(path_lib_src, "csymlib.c")).read()
+-    .replace(
+-      "static int reported_syminfo = 0",
+-      "static int reported_syminfo = 1"))
+-source.append(op.join("#ccp4io_adaptbx", "csymlib.c"))
++if not env_etc.check_syslib('ccp4c')\
++  or not env_etc.check_syslib('mmdb'):
++  build_ccp4io_adaptbx = libtbx.env.under_build("ccp4io_adaptbx")
++  if (not op.isdir(build_ccp4io_adaptbx)):
++    os.mkdir(build_ccp4io_adaptbx)
++    assert op.isdir(build_ccp4io_adaptbx)
++
++  def replace_printf(file_name):
++    full_path = op.join(path_lib_src, file_name)
++    if (not op.isfile(full_path)):
++      full_path = op.join(op.dirname(path_lib_src), "fortran", file_name)
++    result = ["#include <ccp4io_adaptbx/printf_wrappers.h>"]
++    for line in open(full_path).read().splitlines():
++      for key in ["printf", "fprintf"]:
++        matches = list(re.finditer(
++          pattern="[^A-Za-z0-9_]%s[^A-Za-z0-9_]" % key, string=line))
++        if (len(matches) != 0):
++          for m in reversed(matches):
++            s,e = m.start(), m.end()
++            line = line[:s] \
++                 + line[s:e].replace(key, "ccp4io_%s" % key) \
++                 + line[e:]
++      result.append(line)
++    return "\n".join(result)
++  env = env_base.Clone(
++    SHLINKFLAGS=env_etc.shlinkflags)
++  env.Append(CCFLAGS=env_etc.ccp4io_defines)
++  env.Append(SHCCFLAGS=env_etc.ccp4io_defines)
++  env_etc.include_registry.append(
++    env=env,
++    paths=[
++      "#",
++      op.dirname(env_etc.ccp4io_include),
++      env_etc.ccp4io_include,
++      op.join(env_etc.ccp4io_dist, "lib", mmdb_src),
++      op.join(env_etc.ccp4io_dist, "lib", mmdb_src, "mmdb")])
++  env.Append(LIBS=env_etc.libm)
++  if (   op.normcase(op.dirname(env_etc.ccp4io_dist))
++      != op.normcase("ccp4io")):
++    env.Repository(op.dirname(env_etc.ccp4io_dist))
+ 
+-probe_file_name = op.join(path_lib_src, "cmaplib.h")
+-env_etc.ccp4io_has_cmaplib = op.isfile(probe_file_name)
+-if (env_etc.ccp4io_has_cmaplib):
+   c_files.extend(["%s/%s" % (ccp4_src, bn ) for bn in """\
+-cmap_accessor.c
+-cmap_close.c
+-cmap_data.c
+-cmap_header.c
+-cmap_labels.c
+-cmap_open.c
+-cmap_skew.c
+-cmap_stats.c
+-cmap_symop.c
+-""".splitlines()])
++  library_err.c
++  library_file.c
++  library_utils.c
++  ccp4_array.c
++  ccp4_parser.c
++  ccp4_unitcell.c
++  cvecmat.c
++  cmtzlib.c
++  """.splitlines()])
++  open(op.join(build_ccp4io_adaptbx, "csymlib.c"), "w").write(
++    open(op.join(path_lib_src, "csymlib.c")).read()
++      .replace(
++        "static int reported_syminfo = 0",
++        "static int reported_syminfo = 1"))
++  source.append(op.join("#ccp4io_adaptbx", "csymlib.c"))
+ 
+-c_files.extend(["%s/mmdb/%s.cpp" % ( mmdb_src, bn ) for bn in """\
+-bfgs_min
+-file_
+-hybrid_36
+-linalg_
+-machine_
+-math_
+-mattype_
+-mmdb_align
+-mmdb_atom
+-mmdb_bondmngr
+-mmdb_chain
+-mmdb_cifdefs
+-mmdb_coormngr
+-mmdb_cryst
+-mmdb_ficif
+-mmdb_file
+-mmdb_graph
+-mmdb_manager
+-mmdb_mask
+-mmdb_mmcif
+-mmdb_model
+-mmdb_rwbrook
+-mmdb_sbase
+-mmdb_sbase0
+-mmdb_selmngr
+-mmdb_symop
+-mmdb_tables
+-mmdb_title
+-mmdb_uddata
+-mmdb_utils
+-mmdb_xml
+-random_n
+-stream_
+-""".splitlines()])
+-prefix = "#"+op.join(op.basename(env_etc.ccp4io_dist), "lib")
+-for file_name in c_files:
+-  source.append(op.join(prefix, file_name))
++  probe_file_name = op.join(path_lib_src, "cmaplib.h")
++  env_etc.ccp4io_has_cmaplib = op.isfile(probe_file_name)
++  if (env_etc.ccp4io_has_cmaplib):
++    c_files.extend(["%s/%s" % (ccp4_src, bn ) for bn in """\
++  cmap_accessor.c
++  cmap_close.c
++  cmap_data.c
++  cmap_header.c
++  cmap_labels.c
++  cmap_open.c
++  cmap_skew.c
++  cmap_stats.c
++  cmap_symop.c
++  """.splitlines()])
++
++  c_files.extend(["%s/mmdb/%s.cpp" % ( mmdb_src, bn ) for bn in """\
++  bfgs_min
++  file_
++  hybrid_36
++  linalg_
++  machine_
++  math_
++  mattype_
++  mmdb_align
++  mmdb_atom
++  mmdb_bondmngr
++  mmdb_chain
++  mmdb_cifdefs
++  mmdb_coormngr
++  mmdb_cryst
++  mmdb_ficif
++  mmdb_file
++  mmdb_graph
++  mmdb_manager
++  mmdb_mask
++  mmdb_mmcif
++  mmdb_model
++  mmdb_rwbrook
++  mmdb_sbase
++  mmdb_sbase0
++  mmdb_selmngr
++  mmdb_symop
++  mmdb_tables
++  mmdb_title
++  mmdb_uddata
++  mmdb_utils
++  mmdb_xml
++  random_n
++  stream_
++  """.splitlines()])
++  prefix = "#"+op.join(op.basename(env_etc.ccp4io_dist), "lib")
++  for file_name in c_files:
++    source.append(op.join(prefix, file_name))
++
++  need_f_c = (
++       libtbx.env.has_module("solve_resolve")
++    or libtbx.env.find_in_repositories(relative_path="mosflm_fable"))
++  if (need_f_c or os.name != "nt"):
++    source.append(op.join("#ccp4io_adaptbx", "fortran_call_stubs.c"))
++    for file_name in """\
++  ccp4_diskio_f.c
++  ccp4_general.c
++  ccp4_general_f.c
++  ccp4_parser_f.c
++  ccp4_program.c
++  ccp4_unitcell_f.c
++  cmaplib_f.c
++  cmtzlib_f.c
++  csymlib_f.c
++  library_f.c
++  """.splitlines():
++      open(op.join(build_ccp4io_adaptbx, file_name), "w").write(
++        replace_printf(file_name=file_name))
++      source.append(op.join("#ccp4io_adaptbx", file_name))
++    source.append(op.join("#ccp4io_adaptbx", "printf_wrappers.c"))
++  env_etc.ccp4io_lib = "ccp4io"
++  mmdb_path= [ os.path.join( env_etc.ccp4io_dist, "lib", mmdb_src ),
++               os.path.join( env_etc.ccp4io_dist, "lib", mmdb_src, "mmdb" ),
++             ]
++else:
++  env = env_base.Clone(
++    SHLINKFLAGS=env_etc.shlinkflags)
++  env.Append(CCFLAGS=env_etc.ccp4io_defines)
++  env.Append(SHCCFLAGS=env_etc.ccp4io_defines)
++  env_etc.ccp4io_lib = ["ccp4io", "mmdb", "ccp4c"]
++  mmdb_path= []
+ 
+ ssm_prefix = "#"+op.join(op.basename(env_etc.ccp4io_dist), "lib", "ssm")
+ ssm_sources = """\
+@@ -159,46 +193,20 @@ ssm_superpose.cpp
+ """.splitlines()
+ source.extend( [ op.join( ssm_prefix, f ) for f in ssm_sources ] )
+ 
+-need_f_c = (
+-     libtbx.env.has_module("solve_resolve")
+-  or libtbx.env.find_in_repositories(relative_path="mosflm_fable"))
+-if (need_f_c or os.name != "nt"):
+-  source.append(op.join("#ccp4io_adaptbx", "fortran_call_stubs.c"))
+-  for file_name in """\
+-ccp4_diskio_f.c
+-ccp4_general.c
+-ccp4_general_f.c
+-ccp4_parser_f.c
+-ccp4_program.c
+-ccp4_unitcell_f.c
+-cmaplib_f.c
+-cmtzlib_f.c
+-csymlib_f.c
+-library_f.c
+-""".splitlines():
+-    open(op.join(build_ccp4io_adaptbx, file_name), "w").write(
+-      replace_printf(file_name=file_name))
+-    source.append(op.join("#ccp4io_adaptbx", file_name))
+-  source.append(op.join("#ccp4io_adaptbx", "printf_wrappers.c"))
+-
+ # static library for solve_resolve
+ env.StaticLibrary(target='#lib/ccp4io', source=source)
+-env_etc.ccp4io_lib = "ccp4io"
+ 
+ if (    libtbx.env.has_module("boost")
+     and not env_etc.no_boost_python):
+   Import( "env_no_includes_boost_python_ext" )
+   sources = [ "#ccp4io_adaptbx/ext.cpp" ]
+   env_ext = env_no_includes_boost_python_ext.Clone()
+-  env_ext.Prepend( LIBS = "ccp4io" )
++  env_ext.Prepend( LIBS = env_etc.ccp4io_lib )
+   env_etc.include_registry.append(
+     env = env_ext,
+-    paths = [
+-      os.path.join( env_etc.ccp4io_dist, "lib", mmdb_src ),
+-      os.path.join( env_etc.ccp4io_dist, "lib", mmdb_src, "mmdb" ),
+-      os.path.join( env_etc.ccp4io_dist, "lib", "ssm"),
+-      env_etc.boost_include,
+-      env_etc.python_include,
+-      ]
++    paths = mmdb_path + [ os.path.join( env_etc.ccp4io_dist, "lib", "ssm"),
++                          env_etc.boost_include,
++                          env_etc.python_include,
++                        ]
+     )
+   env_ext.SharedLibrary( target = "#lib/ccp4io_adaptbx_ext", source = sources )
+diff --git a/cctbx_sources/cctbx/SConscript b/cctbx_sources/cctbx/SConscript
+index af767ae..6ce770c 100644
+--- a/cctbx_sources/cctbx/SConscript
++++ b/cctbx_sources/cctbx/SConscript
+@@ -106,7 +106,7 @@ if (not env_etc.no_boost_python):
+   Import("env_no_includes_boost_python_ext")
+ 
+   env_cctbx_boost_python_ext = env_no_includes_boost_python_ext.Clone()
+-  env_cctbx_boost_python_ext.Prepend(LIBS=["scitbx_boost_python"])
++  env_cctbx_boost_python_ext.Prepend(LIBS=[env_etc.scitbx_boost_python])
+   env_etc.include_registry.append(
+     env=env_cctbx_boost_python_ext,
+     paths=env_etc.cctbx_common_includes + [env_etc.python_include])
+diff --git a/cctbx_sources/clipper_adaptbx/SConscript b/cctbx_sources/clipper_adaptbx/SConscript
+index 9cce49e..c39047f 100644
+--- a/cctbx_sources/clipper_adaptbx/SConscript
++++ b/cctbx_sources/clipper_adaptbx/SConscript
+@@ -3,54 +3,63 @@ Import("env_base", "env_etc")
+ 
+ env_etc.clipper_dist = libtbx.env.dist_path("clipper")
+ env_etc.clipper_include = env_etc.clipper_dist
++# This way the compiler looks in the standard location for includes
++# should work on all platforms
++env_etc.clipper_sysinclude = ''
+ 
+ env = env_base.Clone(
+   SHLINKFLAGS=env_etc.shlinkflags,
+   LIBS=env_etc.libm)
+-env.Prepend(CPPPATH=[env_etc.clipper_include])
+-
+-if (env_etc.static_libraries): builder = env.StaticLibrary
+-else:                          builder = env.SharedLibrary
+-builder(target='#lib/clipper',
+-  source = ["../clipper/clipper/core/"+file_name for file_name in """
+-  atomsf.cpp
+-  cell.cpp
+-  clipper_memory.cpp
+-  clipper_message.cpp
+-  clipper_stats.cpp
+-  clipper_types.cpp
+-  clipper_util.cpp
+-  container.cpp
+-  container_hkl.cpp
+-  container_map.cpp
+-  container_types.cpp
+-  coords.cpp
+-  derivs.cpp
+-  hkl_compute.cpp
+-  hkl_data.cpp
+-  hkl_datatypes.cpp
+-  hkl_info.cpp
+-  hkl_lookup.cpp
+-  hkl_operators.cpp
+-  map_interp.cpp
+-  map_utils.cpp
+-  nxmap.cpp
+-  nxmap_operator.cpp
+-  ramachandran.cpp
+-  resol_basisfn.cpp
+-  resol_fn.cpp
+-  resol_targetfn.cpp
+-  rotation.cpp
+-  spacegroup.cpp
+-  spacegroup_data.cpp
+-  symop.cpp
+-  xmap.cpp
+-""".split()])
+-# fftmap_sparse.cpp
+-# fftmap.cpp
++if env_etc.check_syslib('clipper-core') and \
++    env_etc.check_syslib('clipper-contrib'):
++  env.Prepend(CPPPATH=[env_etc.clipper_sysinclude])
++  env_etc.clipper_libs=['clipper-core', 'clipper-contrib']
++  env_etc.has_clipper_contrib = True
++else:
++  env.Prepend(CPPPATH=[env_etc.clipper_include])
++  env_etc.clipper_libs=['clipper',]
++  if (env_etc.static_libraries): builder = env.StaticLibrary
++  else:                          builder = env.SharedLibrary
++  builder(target='#lib/'+env_etc.clipper_libs[0],
++    source = ["../clipper/clipper/core/"+file_name for file_name in """
++    atomsf.cpp
++    cell.cpp
++    clipper_memory.cpp
++    clipper_message.cpp
++    clipper_stats.cpp
++    clipper_types.cpp
++    clipper_util.cpp
++    container.cpp
++    container_hkl.cpp
++    container_map.cpp
++    container_types.cpp
++    coords.cpp
++    derivs.cpp
++    hkl_compute.cpp
++    hkl_data.cpp
++    hkl_datatypes.cpp
++    hkl_info.cpp
++    hkl_lookup.cpp
++    hkl_operators.cpp
++    map_interp.cpp
++    map_utils.cpp
++    nxmap.cpp
++    nxmap_operator.cpp
++    ramachandran.cpp
++    resol_basisfn.cpp
++    resol_fn.cpp
++    resol_targetfn.cpp
++    rotation.cpp
++    spacegroup.cpp
++    spacegroup_data.cpp
++    symop.cpp
++    xmap.cpp
++  """.split()])
++  # fftmap_sparse.cpp
++  # fftmap.cpp
+ 
+ env_exe = env.Clone()
+-env_exe.Prepend(LIBS=["clipper"])
++env_exe.Prepend(LIBS=[env_etc.clipper_libs[0]])
+ 
+ exe = env_exe.Program(
+   target='#exe_dev/'+env["PROGPREFIX"]+'clipper.symtest'
+@@ -77,6 +86,7 @@ if (hasattr(env_etc, "cctbx_include")):
+       env=env_clipper_boost_python_ext,
+       paths=[
+         env_etc.clipper_include,
++        env_etc.clipper_sysinclude,
+         env_etc.libtbx_include,
+         env_etc.cctbx_include,
+         env_etc.scitbx_include,
+diff --git a/cctbx_sources/clipper_adaptbx/clipper/SConscript b/cctbx_sources/clipper_adaptbx/clipper/SConscript
+index 9f79f83..1911eb1 100644
+--- a/cctbx_sources/clipper_adaptbx/clipper/SConscript
++++ b/cctbx_sources/clipper_adaptbx/clipper/SConscript
+@@ -1,6 +1,10 @@
+-Import("env_clipper_boost_python_ext")
++Import("env_clipper_boost_python_ext", "env_etc")
+ env = env_clipper_boost_python_ext.Clone()
+-env.Prepend(LIBS=["clipper", "cctbx"])
++env.Prepend(LIBS=env_etc.clipper_libs+["cctbx"])
++if (env_etc.has_clipper_contrib):
++  clipper_contrib_files = []
++else:
++  clipper_contrib_files = ["../../clipper/clipper/contrib/sfweight.cpp",]
+ env.SharedLibrary(
+   target="#lib/clipper_ext",
+   source=[
+@@ -8,4 +12,4 @@ env.SharedLibrary(
+     "hendrickson_lattman_bpl.cpp",
+     "sigmaa_bpl.cpp",
+     "../../clipper/clipper/contrib/sfweight.cpp",
+-    "../../clipper/clipper/cctbx/clipper_cctbx.cpp"])
++    "../../clipper/clipper/cctbx/clipper_cctbx.cpp"]+clipper_contrib_files)
+diff --git a/cctbx_sources/gltbx/SConscript b/cctbx_sources/gltbx/SConscript
+index 4b2213d..04e0654 100644
+--- a/cctbx_sources/gltbx/SConscript
++++ b/cctbx_sources/gltbx/SConscript
+@@ -12,14 +12,15 @@ env_etc.gltbx_common_includes = [
+   env_etc.scitbx_include,
+   env_etc.boost_include,
+ ]
+-if (gl2ps_path is not None):
+-  env_etc.gltbx_common_includes.append(gl2ps_path)
++if not env_etc.check_syslib('gl2ps', extra_libs='GL'):
++  if (gl2ps_path is not None):
++    env_etc.gltbx_common_includes.append(gl2ps_path)
+ 
+ if (not env_etc.no_boost_python):
+   Import("env_base", "env_no_includes_boost_python_ext")
+   trial_env = env_base.Clone()
+   env = env_no_includes_boost_python_ext.Clone()
+-  env.Prepend(LIBS=["scitbx_boost_python"])
++  env.Prepend(LIBS=[env_etc.scitbx_boost_python])
+   if (env_etc.compiler == "win32_cl"):
+     for e in [trial_env, env]:
+       e.Append(LIBS=["glu32", "opengl32"])
+@@ -79,10 +80,15 @@ if (not env_etc.no_boost_python):
+         source=source)
+     env_util = env
+     source = ["util_ext.cpp"]
+-    if (gl2ps_path is not None):
+-      source.append("#gui_resources/gl2ps/gl2ps.c")
+-      env_util = env.Clone()
+-      env_util.Append(SHCXXFLAGS=["-DGLTBX_HAVE_GL2PS"])
++    if not env_etc.check_syslib('gl2ps', extra_libs='GL'):
++      if (gl2ps_path is not None):
++        source.append("#gui_resources/gl2ps/gl2ps.c")
++        env_util = env.Clone()
++        env_util.Append(SHCXXFLAGS=["-DGLTBX_HAVE_GL2PS"])
++    else:
++        env_util = env.Clone()
++        env_util.Append(SHCXXFLAGS=["-DGLTBX_HAVE_GL2PS"])
++        env_util.Append(LIBS=["gl2ps"])
+     env_util.SharedLibrary(
+       target="#lib/gltbx_util_ext",
+       source=source)
+diff --git a/cctbx_sources/iotbx/cif/boost_python/SConscript b/cctbx_sources/iotbx/cif/boost_python/SConscript
+index 49837af..2833ff1 100644
+--- a/cctbx_sources/iotbx/cif/boost_python/SConscript
++++ b/cctbx_sources/iotbx/cif/boost_python/SConscript
+@@ -34,15 +34,18 @@ antlr3_src_files = [
+ ]
+ 
+ prefix = "#ucif/antlr3/src"
+-source = [os.path.join(prefix, file_name) for file_name in antlr3_src_files]
++if not env_etc.check_syslib('antlr3c'):
++  source = [os.path.join(prefix, file_name) for file_name in antlr3_src_files]
++  env_etc.include_registry.append(
++    env=env,
++    paths=[antlr3_include, antlr3_dist])
++else:
++  source = []
++  env.Append(LIBS=['antlr3c'])
+ source.extend([
+   "cif_ext.cpp",
+   "#ucif/cifParser.cpp",
+   "#ucif/cifLexer.cpp",
+ ])
+ 
+-env_etc.include_registry.append(
+-  env=env,
+-  paths=[antlr3_include, antlr3_dist])
+-
+ env.SharedLibrary(target="#lib/iotbx_cif_ext", source=source)
+diff --git a/cctbx_sources/iotbx/mtz/SConscript b/cctbx_sources/iotbx/mtz/SConscript
+index c0a4bb0..cd539e6 100644
+--- a/cctbx_sources/iotbx/mtz/SConscript
++++ b/cctbx_sources/iotbx/mtz/SConscript
+@@ -22,7 +22,8 @@ if (not env_etc.no_boost_python):
+   env = env_iotbx_boost_python_ext.Clone()
+   env.Append(CXXFLAGS=env_etc.ccp4io_defines)
+   env.Append(SHCXXFLAGS=env_etc.ccp4io_defines)
+-  env.Prepend(LIBS=["iotbx_mtz", "cctbx", ccp4io_lib, "scitbx_boost_python"])
++  env.Prepend(LIBS=["iotbx_mtz", "cctbx", ccp4io_lib,
++                     env_etc.scitbx_boost_python])
+   env_etc.enable_more_warnings(env=env)
+   env.SharedLibrary(
+     target="#lib/iotbx_mtz_ext",
+diff --git a/cctbx_sources/iotbx/pdb/SConscript b/cctbx_sources/iotbx/pdb/SConscript
+index 6af2664..9b89fe1 100644
+--- a/cctbx_sources/iotbx/pdb/SConscript
++++ b/cctbx_sources/iotbx/pdb/SConscript
+@@ -33,7 +33,7 @@ env.Program(target="hybrid_36_fem", source=["hybrid_36_fem.cpp"])
+ if (not env_etc.no_boost_python):
+   Import("env_iotbx_boost_python_ext")
+   env = env_iotbx_boost_python_ext.Clone()
+-  env.Prepend(LIBS=["iotbx_pdb", "cctbx", "scitbx_boost_python"])
++  env.Prepend(LIBS=["iotbx_pdb", "cctbx", env_etc.scitbx_boost_python])
+   env_etc.enable_more_warnings(env=env)
+   env.SharedLibrary(
+     target="#lib/iotbx_pdb_ext",
+diff --git a/cctbx_sources/libtbx/SConscript b/cctbx_sources/libtbx/SConscript
+index debf569..429c44b 100644
+--- a/cctbx_sources/libtbx/SConscript
++++ b/cctbx_sources/libtbx/SConscript
+@@ -4,7 +4,7 @@ from libtbx import easy_run
+ from libtbx.utils import getenv_bool
+ from libtbx.str_utils import show_string
+ from libtbx.path import norm_join, full_command_path
+-import sys, os
++import sys, os, re
+ op = os.path
+ 
+ if (hasattr(Environment, "Clone")):
+@@ -1018,4 +1018,88 @@ def enable_cuda_if_possible():
+ enable_openmp_if_possible()
+ enable_cuda_if_possible()
+ 
++env_etc.use_system_libs = False
++def check_syslib(lib, extra_libs=None):
++  """ Check if a system library is available """
++  if not env_etc.use_system_libs:
++    return False
++  env_syslib = env_base.Clone(LIBS=extra_libs)
++  conf = env_syslib.Configure()
++  if not conf.CheckLib(library=lib):
++    print 'Could not find %s library!'%(lib)
++    conf.Finish()
++    return False
++  else:
++    conf.Finish()
++    return True
++env_etc.check_syslib = check_syslib
++
++env_etc.py_lib = 'python%s.%s'%(sys.version[0], sys.version[2])
++
++if (libtbx.env.build_options.use_system_libs):
++  env_etc.use_system_libs = True
++
++deb_py_str = '-py%s%s'%(sys.version[0], sys.version[2])
++gentoo_py_str = '-%s.%s'%(sys.version[0], sys.version[2])
++# This list can be extended by other distro's
++py_str_lst = [deb_py_str, gentoo_py_str]
++
++for py_str in py_str_lst:
++  if env_etc.check_syslib('boost_python%s'%py_str,
++      extra_libs=env_etc.py_lib):
++    env_etc.boost_python = 'boost_python%s'%py_str
++    env_etc.scitbx_boost_python = 'scitbx_boost_python%s'%py_str
++    break
++  else:
++    env_etc.boost_python = 'boost_python'
++    env_etc.scitbx_boost_python = 'scitbx_boost_python'
++
++env_etc.prefix = libtbx.env.build_options.install_prefix
++env_etc.destdir = libtbx.env.build_options.install_destdir
++env_etc.libdir = libtbx.env.build_options.libdir
++env_etc.install_path = os.path.abspath(env_etc.destdir + '/' + env_etc.prefix)
++env_etc.binpath = os.path.join(env_etc.install_path, 'bin')
++env_etc.libpath = os.path.abspath(env_etc.install_path + '/' + env_etc.libdir)
++env_etc.inclpath = os.path.join(env_etc.install_path, 'include')
++env_etc.rpath = os.path.join(env_etc.prefix, 'lib')
++
++def create_install_targets():
++  cwd = os.getcwd()
++  rp = libtbx.env.repository_paths
++  lib_dir = '%s%s'%(abs(libtbx.env.lib_path), env_etc.rpath)
++  exe_dev = libtbx.env.under_build("exe_dev")
++  include_path = libtbx.env.include_path
++  if not os.path.exists(lib_dir):
++    os.makedirs(lib_dir)
++  rp = list(rp)
++  rp.append(lib_dir)
++  rp.append(include_path)
++  for p in rp:
++    if isinstance(p, str):
++      src_dir = p
++    else:
++      src_dir = abs(p)
++    os.chdir(src_dir)
++    dest = None
++    for root, dirnames, filenames in os.walk('.'):
++      for filename in filenames:
++        if re.match('^lib.*\.(so.*|dylib.*|la|a)$', filename, flags=re.IGNORECASE):
++          dest = os.path.join(env_etc.libpath, root)
++          src = os.path.join(src_dir, root, filename)
++          env_base.Install(dest, src)
++          env_base.Alias("install-shlib", dest)
++        if re.match('^.*\.(h|hpp)$', filename, flags=re.IGNORECASE):
++          dest = os.path.join(env_etc.inclpath, root)
++          src = os.path.join(src_dir, root, filename)
++          env_base.Install(dest, src)
++          env_base.Alias("install-header", dest)
++  dest = env_etc.binpath
++  env_base.Install(dest, Glob('%s/*'%(exe_dev)))
++  env_base.Alias("install-bin", dest)
++  Alias('install', ['install-header', 'install-shlib', 'install-bin'])
++  os.chdir(cwd)
++
++if 'install' in COMMAND_LINE_TARGETS:
++  create_install_targets()
++
+ Export("env_base", "env_etc")
+diff --git a/cctbx_sources/libtbx/env_config.py b/cctbx_sources/libtbx/env_config.py
+index c3e1c7d..0885527 100644
+--- a/cctbx_sources/libtbx/env_config.py
++++ b/cctbx_sources/libtbx/env_config.py
+@@ -701,6 +701,10 @@ Wait for the command to finish, then try again.""" % vars())
+         precompile_headers=command_line.options.precompile_headers,
+         static_libraries=command_line.options.static_libraries,
+         static_exe=command_line.options.static_exe,
++        use_system_libs=command_line.options.use_system_libs,
++        install_prefix=command_line.options.install_prefix,
++        libdir=command_line.options.libdir,
++        install_destdir=command_line.options.install_destdir,
+         scan_boost=command_line.options.scan_boost,
+         write_full_flex_fwd_h=command_line.options.write_full_flex_fwd_h,
+         boost_python_no_py_signatures
+@@ -1759,6 +1763,10 @@ class build_options:
+         warning_level,
+         static_libraries,
+         static_exe,
++        use_system_libs,
++        install_prefix,
++        libdir,
++        install_destdir,
+         scan_boost,
+         write_full_flex_fwd_h=default_write_full_flex_fwd_h,
+         build_boost_python_extensions=default_build_boost_python_extensions,
+@@ -1822,6 +1830,10 @@ class build_options:
+     print >> f, "Boost threads enabled:", self.enable_boost_threads
+     print >> f, "Enable OpenMP if possible:", self.enable_openmp_if_possible
+     print >> f, "Enable CUDA:", self.enable_cuda
++    print >> f, "Use System Libraries:", self.use_system_libs
++    print >> f, "Install Prefix:", self.install_prefix
++    print >> f, "Libdir:", self.libdir
++    print >> f, "Install Destdir:", self.install_destdir
+     print >> f, "Use opt_resources if available:", self.opt_resources
+     print >> f, "Use environment flags:", self.use_environment_flags
+     if( self.use_environment_flags ):
+@@ -1940,6 +1952,28 @@ class pre_process_args:
+         action="store_true",
+         default=False,
+         help="link all executables statically (implies --static_libraries)")
++      parser.option(None, "--use_system_libs",
++        action="store_true",
++        default=False,
++        help="Use system Libraries to build.")
++      parser.option(None, "--install_destdir",
++        type="string",
++        action="store",
++        default="",
++        help="sets the destdir for the install targets.",
++        metavar="DIRECTORY")
++      parser.option(None, "--libdir",
++        type="string",
++        action="store",
++        default="lib",
++        help="sets the libdir relative to the PREFIX for the install targets. Default: lib",
++        metavar="DIRECTORY")
++      parser.option(None, "--install_prefix",
++        type="string",
++        action="store",
++        default="/usr/local",
++        help="sets the prefix for the install targets. Default: /usr/local",
++        metavar="DIRECTORY")
+       parser.option(None, "--scan_boost",
+         action="store_true",
+         default=False,
+diff --git a/cctbx_sources/mmtbx/den/SConscript b/cctbx_sources/mmtbx/den/SConscript
+index 2d3ce36..1a2b171 100644
+--- a/cctbx_sources/mmtbx/den/SConscript
++++ b/cctbx_sources/mmtbx/den/SConscript
+@@ -3,7 +3,7 @@ Import("env_etc")
+ if (not env_etc.no_boost_python):
+   Import("env_iotbx_boost_python_ext")
+   env = env_iotbx_boost_python_ext.Clone()
+-  env.Prepend(LIBS=["cctbx", "scitbx_boost_python"])
++  env.Prepend(LIBS=["cctbx", env_etc.scitbx_boost_python])
+   env_etc.enable_more_warnings(env=env)
+   env.SharedLibrary(
+     target="#lib/mmtbx_den_restraints_ext",
+diff --git a/cctbx_sources/mmtbx/geometry_restraints/SConscript b/cctbx_sources/mmtbx/geometry_restraints/SConscript
+index 222d5f6..e11e5f9 100644
+--- a/cctbx_sources/mmtbx/geometry_restraints/SConscript
++++ b/cctbx_sources/mmtbx/geometry_restraints/SConscript
+@@ -3,7 +3,7 @@ Import("env_etc")
+ if (not env_etc.no_boost_python):
+   Import("env_iotbx_boost_python_ext")
+   env = env_iotbx_boost_python_ext.Clone()
+-  env.Prepend(LIBS=["cctbx", "scitbx_boost_python"])
++  env.Prepend(LIBS=["cctbx", env_etc.scitbx_boost_python])
+   env_etc.enable_more_warnings(env=env)
+   env.SharedLibrary(
+     target="#lib/mmtbx_hbond_restraints_ext",
+diff --git a/cctbx_sources/mmtbx/secondary_structure/SConscript b/cctbx_sources/mmtbx/secondary_structure/SConscript
+index 7e82b43..5698af5 100644
+--- a/cctbx_sources/mmtbx/secondary_structure/SConscript
++++ b/cctbx_sources/mmtbx/secondary_structure/SConscript
+@@ -3,7 +3,7 @@ Import("env_etc")
+ if (not env_etc.no_boost_python):
+   Import("env_iotbx_boost_python_ext")
+   env = env_iotbx_boost_python_ext.Clone()
+-  env.Prepend(LIBS=["cctbx", "scitbx_boost_python"])
++  env.Prepend(LIBS=["cctbx", env_etc.scitbx_boost_python])
+   env_etc.enable_more_warnings(env=env)
+   env.SharedLibrary(
+     target="#lib/mmtbx_secondary_structure_ext",
+diff --git a/cctbx_sources/rstbx/SConscript b/cctbx_sources/rstbx/SConscript
+index a1ab8e5..e2958a1 100644
+--- a/cctbx_sources/rstbx/SConscript
++++ b/cctbx_sources/rstbx/SConscript
+@@ -39,7 +39,7 @@ if (not env_etc.no_boost_python):
+   Import("env_boost_python_ext")
+   env_rstbx_boost_python_ext = env_boost_python_ext.Clone()
+   env_rstbx_boost_python_ext.Prepend(
+-                 LIBS=["rstbx", "cctbx", "scitbx_boost_python"])
++                 LIBS=["rstbx", "cctbx", env_etc.scitbx_boost_python])
+   env_rstbx_boost_python_ext.SharedLibrary(
+                  target="#lib/rstbx_ext", source="ext.cpp")
+   env_rstbx_boost_python_ext.SharedLibrary(
+diff --git a/cctbx_sources/scitbx/SConscript b/cctbx_sources/scitbx/SConscript
+index 9199ae0..6045fbc 100644
+--- a/cctbx_sources/scitbx/SConscript
++++ b/cctbx_sources/scitbx/SConscript
+@@ -28,7 +28,7 @@ SConscript("sparse/tests/SConscript")
+ if (not env_etc.no_boost_python):
+   Import("env_no_includes_boost_python_ext")
+   env_scitbx_boost_python_ext = env_no_includes_boost_python_ext.Clone()
+-  env_scitbx_boost_python_ext.Prepend(LIBS=["scitbx_boost_python"])
++  env_scitbx_boost_python_ext.Prepend(LIBS=[env_etc.scitbx_boost_python])
+   env_etc.include_registry.append(
+     env=env_scitbx_boost_python_ext,
+     paths=env_etc.scitbx_common_includes + [env_etc.python_include])
+diff --git a/cctbx_sources/scitbx/boost_python/SConscript b/cctbx_sources/scitbx/boost_python/SConscript
+index eda7b03..1f396e5 100644
+--- a/cctbx_sources/scitbx/boost_python/SConscript
++++ b/cctbx_sources/scitbx/boost_python/SConscript
+@@ -7,7 +7,7 @@ env_etc.enable_more_warnings(env=env)
+ env.Append(CXXFLAGS=env_etc.cxxflags_bpl_defines_base)
+ env.Append(SHCXXFLAGS=env_etc.cxxflags_bpl_defines_base)
+ env.Append(LIBPATH=env_etc.libpath_python)
+-env.Append(LIBS=["boost_python"] + env_etc.libs_python)
++env.Append(LIBS=[env_etc.boost_python] + env_etc.libs_python)
+ env_etc.include_registry.append(
+   env=env,
+   paths=env_etc.scitbx_common_includes + [env_etc.python_include])
+@@ -20,5 +20,5 @@ lib_scitbx_boost_python_sources = [
+ if (env_etc.static_libraries): builder = env.StaticLibrary
+ else:                          builder = env.SharedLibrary
+ builder(
+-  target="#lib/scitbx_boost_python",
++  target="#lib/%s"%env_etc.scitbx_boost_python,
+   source=lib_scitbx_boost_python_sources)
+diff --git a/cctbx_sources/smtbx/refinement/boost_python/SConscript b/cctbx_sources/smtbx/refinement/boost_python/SConscript
+index 0387e1d..5144996 100644
+--- a/cctbx_sources/smtbx/refinement/boost_python/SConscript
++++ b/cctbx_sources/smtbx/refinement/boost_python/SConscript
+@@ -1,6 +1,6 @@
+-Import("env_smtbx_boost_python_ext")
++Import("env_smtbx_boost_python_ext", "env_etc")
+ env = env_smtbx_boost_python_ext.Clone()
+-env.Prepend(LIBS=["smtbx_refinement_constraints", "scitbx_boost_python"])
++env.Prepend(LIBS=["smtbx_refinement_constraints", env_etc.scitbx_boost_python])
+ env.SharedLibrary(target="#lib/smtbx_refinement_least_squares_ext", source=[
+   "least_squares_ext.cpp",
+   "weighting_schemes.cpp",
+diff --git a/cctbx_sources/smtbx/refinement/constraints/boost_python/SConscript b/cctbx_sources/smtbx/refinement/constraints/boost_python/SConscript
+index 009d288..1eb176b 100644
+--- a/cctbx_sources/smtbx/refinement/constraints/boost_python/SConscript
++++ b/cctbx_sources/smtbx/refinement/constraints/boost_python/SConscript
+@@ -1,5 +1,5 @@
+-Import("env_smtbx_boost_python_ext")
++Import("env_smtbx_boost_python_ext", "env_etc")
+ env = env_smtbx_boost_python_ext.Clone()
+-env.Prepend(LIBS=["smtbx_refinement_constraints", "scitbx_boost_python"])
++env.Prepend(LIBS=["smtbx_refinement_constraints", env_etc.scitbx_boost_python])
+ env.SharedLibrary(target="#lib/smtbx_refinement_constraints_ext",
+                   source=Glob("*.cpp"))
+diff --git a/cctbx_sources/spotfinder/SConscript b/cctbx_sources/spotfinder/SConscript
+index 1d280d4..1d73677 100644
+--- a/cctbx_sources/spotfinder/SConscript
++++ b/cctbx_sources/spotfinder/SConscript
+@@ -54,7 +54,7 @@ if (not env_etc.no_boost_python):
+   Import("env_no_includes_boost_python_ext")
+ 
+   env_spotfinder_boost_python_ext = env_no_includes_boost_python_ext.Clone()
+-  env_spotfinder_boost_python_ext.Prepend(LIBS=[ "scitbx_boost_python"])
++  env_spotfinder_boost_python_ext.Prepend(LIBS=[ env_etc.scitbx_boost_python ])
+   env_etc.include_registry.append(
+     env=env_spotfinder_boost_python_ext,
+     paths=env_etc.spotfinder_common_includes + [env_etc.python_include])

diff --git a/sci-libs/cctbx/files/2012.05.08.2305/0007-adding-shlib-versioning.patch b/sci-libs/cctbx/files/2012.05.08.2305/0007-adding-shlib-versioning.patch
new file mode 100644
index 0000000..fd1888e
--- /dev/null
+++ b/sci-libs/cctbx/files/2012.05.08.2305/0007-adding-shlib-versioning.patch
@@ -0,0 +1,208 @@
+From: Radostan Riedel <raybuntu@××××××××××.com>
+Date: Mon, 23 Jul 2012 18:33:07 +0200
+Subject: adding-shlib-versioning
+
+---
+ cctbx_sources/boost_adaptbx/SConscript |    3 +
+ cctbx_sources/libtbx/SConscript        |  115 +++++++++++++++++++++++++++++---
+ cctbx_sources/libtbx/env_config.py     |    7 ++
+ 3 files changed, 116 insertions(+), 9 deletions(-)
+
+diff --git a/cctbx_sources/boost_adaptbx/SConscript b/cctbx_sources/boost_adaptbx/SConscript
+index 68cac89..dedbb05 100644
+--- a/cctbx_sources/boost_adaptbx/SConscript
++++ b/cctbx_sources/boost_adaptbx/SConscript
+@@ -58,6 +58,9 @@ if (not env_etc.no_boost_python):
+     SHLINKFLAGS=env_etc.shlinkflags_bpl,
+     SHLIBPREFIX="",
+     LIBS=[env_etc.boost_python] + env_etc.libs_python + env_etc.libm)
++  if (libtbx.env.build_options.libtoolize):
++    # Need to unset libtool since it does not support linking python-ext
++    env_etc.unset_libtool(env_no_includes_boost_python_ext)
+   env_no_includes_boost_python_ext.Append(
+     LIBPATH=env_etc.libpath_python)
+   env_no_includes_boost_python_ext.Append(
+diff --git a/cctbx_sources/libtbx/SConscript b/cctbx_sources/libtbx/SConscript
+index 429c44b..58bdd30 100644
+--- a/cctbx_sources/libtbx/SConscript
++++ b/cctbx_sources/libtbx/SConscript
+@@ -1061,16 +1061,99 @@ env_etc.install_path = os.path.abspath(env_etc.destdir + '/' + env_etc.prefix)
+ env_etc.binpath = os.path.join(env_etc.install_path, 'bin')
+ env_etc.libpath = os.path.abspath(env_etc.install_path + '/' + env_etc.libdir)
+ env_etc.inclpath = os.path.join(env_etc.install_path, 'include')
+-env_etc.rpath = os.path.join(env_etc.prefix, 'lib')
++env_etc.rpath = os.path.abspath(env_etc.prefix + '/' + env_etc.libdir)
++
++def set_libtool(env):
++  # Versioning can be provided by appending "-version-info 3:12:1" to SHLINKFLAGS
++  # Please see:
++  # http://www.gnu.org/software/libtool/manual/html_node/Updating-version-info.html
++  # for reference. Otherwise it will be set to 0:0:0
++  env_etc.shobjsuffix_save = env['SHOBJSUFFIX']
++  env_etc.SharedLibBuilder_save = env['BUILDERS']['SharedLibrary']
++  env.Replace(
++    SHLINKFLAGS='-rpath ' + env_etc.rpath,
++    SHOBJSUFFIX='.lo',
++    SHLIBSUFFIX='.la',
++  )
++  LIBTOOLCOM = 'libtool  --mode=compile --tag='
++  LIBTOOLCCOM = LIBTOOLCOM + 'CC '
++  LIBTOOLCXXCOM = LIBTOOLCOM + 'CXX '
++  LIBTOOLLINK = 'libtool  --mode=link --tag=CXX '
++  ShCAction = SCons.Action.Action(LIBTOOLCCOM + "$SHCCCOM", "$SHCCCOMSTR")
++  ShCXXAction = SCons.Action.Action(LIBTOOLCXXCOM + "$SHCXXCOM", "$SHCXXCOMSTR")
++  ShLinkAction = SCons.Action.Action(LIBTOOLLINK + "$SHLINKCOM", "$SHLINKCOMSTR")
++  libtool_install = 'libtool --mode=install install -D ${TARGET.abspath} %s%s/${TARGET.file}'%(abs(libtbx.env.lib_path), env_etc.rpath)
++
++  action_list = [ SCons.Defaults.SharedCheck,
++                  ShLinkAction,
++                  libtool_install,
++                ]
++  CSuffixes = SCons.Tool.cc.CSuffixes
++  # Can't import SCons.Tool.c++.CSuffixes because of that 'c++'
++  CXXSuffixes = ['.cpp', '.cc', '.cxx', '.c++', '.C++', '.mm']
++  shared_obj = SCons.Builder.Builder(action = {},
++                                     emitter = {},
++                                     prefix = '$SHOBJPREFIX',
++                                     suffix = '$SHOBJSUFFIX',
++                                     src_builder = ['CFile', 'CXXFile'],
++                                     source_scanner = SourceFileScanner,
++                                     single_source = 1)
++  for suffix in CXXSuffixes:
++      shared_obj.add_action(suffix, ShCXXAction)
++      shared_obj.add_emitter(suffix, SCons.Defaults.SharedObjectEmitter)
++  for suffix in CSuffixes:
++      shared_obj.add_action(suffix, ShCAction)
++      shared_obj.add_emitter(suffix, SCons.Defaults.SharedObjectEmitter)
++
++  LibtoolBuilder = SCons.Builder.Builder(action = action_list,
++                                     emitter = "$SHLIBEMITTER",
++                                     prefix = '$SHLIBPREFIX',
++                                     suffix = '$SHLIBSUFFIX',
++                                     target_scanner = ProgramScanner,
++                                     src_suffix = '$SHOBJSUFFIX',
++                                     src_builder = shared_obj)
++
++  from SCons.Tool.install import add_targets_to_INSTALLED_FILES
++  LibtoolInstall = SCons.Builder.Builder(
++                        action         = 'libtool --mode=install install -D ${SOURCE.abspath} ${TARGET.abspath}',
++                        target_factory = env.fs.Entry,
++                        source_factory = env.fs.Entry,
++                        multi          = 1,
++                        emitter        = [ add_targets_to_INSTALLED_FILES, ],
++                        name           = 'LibtoolInstall')
++
++  env['BUILDERS']['LibtoolInstall'] = LibtoolInstall
++
++  lib_dir = '%s%s'%(abs(libtbx.env.lib_path), env_etc.rpath)
++  if not os.path.exists(lib_dir):
++    os.makedirs(lib_dir)
++  libtool_install_path = '#lib' + env_etc.rpath
++  env.Append(LIBPATH=libtool_install_path)
++  env['BUILDERS']['SharedLibrary'] = LibtoolBuilder
++env_etc.set_libtool = set_libtool
++
++def unset_libtool(env):
++  env['BUILDERS']['SharedLibrary'] = env_etc.SharedLibBuilder_save
++  env.Replace(
++  SHOBJSUFFIX=env_etc.shobjsuffix_save,
++  )
++env_etc.unset_libtool = unset_libtool
++
++if (libtbx.env.build_options.libtoolize):
++  env_etc.shlibsuffix = ".la"
++  env_base.Append(LIBSUFFIXES=[env_etc.shlibsuffix])
++  rpath_link = ['-rpath', env_etc.rpath]
++  env_etc.shlinkflags.extend(rpath_link)
++  if '-shared' in env_etc.shlinkflags:
++    env_etc.shlinkflags.remove('-shared')
++  env_etc.set_libtool(env_base)
+ 
+ def create_install_targets():
+   cwd = os.getcwd()
+   rp = libtbx.env.repository_paths
+-  lib_dir = '%s%s'%(abs(libtbx.env.lib_path), env_etc.rpath)
++  lib_dir = abs(libtbx.env.lib_path)
+   exe_dev = libtbx.env.under_build("exe_dev")
+   include_path = libtbx.env.include_path
+-  if not os.path.exists(lib_dir):
+-    os.makedirs(lib_dir)
+   rp = list(rp)
+   rp.append(lib_dir)
+   rp.append(include_path)
+@@ -1082,17 +1165,31 @@ def create_install_targets():
+     os.chdir(src_dir)
+     dest = None
+     for root, dirnames, filenames in os.walk('.'):
++      # exclude .libs dir
++      if '.libs' in dirnames:
++        dirnames.remove('.libs')
+       for filename in filenames:
+-        if re.match('^lib.*\.(so.*|dylib.*|la|a)$', filename, flags=re.IGNORECASE):
+-          dest = os.path.join(env_etc.libpath, root)
+-          src = os.path.join(src_dir, root, filename)
+-          env_base.Install(dest, src)
+-          env_base.Alias("install-shlib", dest)
++        if not (libtbx.env.build_options.libtoolize):
++          if re.match('^lib.*\.(so|dylib|a)$', filename, flags=re.IGNORECASE):
++            dest = os.path.join(env_etc.libpath, root)
++            src = os.path.join(src_dir, root, filename)
++            env_base.Install(dest, src)
++            env_base.Alias("install-shlib", dest)
++        else:
++          if re.match('^lib.*\.la$', filename, flags=re.IGNORECASE):
++            dest = os.path.join(env_etc.libpath, root, filename)
++            src = os.path.join(src_dir, root, filename)
++            env_base.LibtoolInstall(dest, src)
++            env_base.Alias("install-shlib", dest)
+         if re.match('^.*\.(h|hpp)$', filename, flags=re.IGNORECASE):
+           dest = os.path.join(env_etc.inclpath, root)
+           src = os.path.join(src_dir, root, filename)
+           env_base.Install(dest, src)
+           env_base.Alias("install-header", dest)
++      if src_dir == lib_dir:
++        break
++
++  env_base.Alias("install-shlib", dest)
+   dest = env_etc.binpath
+   env_base.Install(dest, Glob('%s/*'%(exe_dev)))
+   env_base.Alias("install-bin", dest)
+diff --git a/cctbx_sources/libtbx/env_config.py b/cctbx_sources/libtbx/env_config.py
+index 0885527..3d9133e 100644
+--- a/cctbx_sources/libtbx/env_config.py
++++ b/cctbx_sources/libtbx/env_config.py
+@@ -705,6 +705,7 @@ Wait for the command to finish, then try again.""" % vars())
+         install_prefix=command_line.options.install_prefix,
+         libdir=command_line.options.libdir,
+         install_destdir=command_line.options.install_destdir,
++        libtoolize=command_line.options.libtoolize,
+         scan_boost=command_line.options.scan_boost,
+         write_full_flex_fwd_h=command_line.options.write_full_flex_fwd_h,
+         boost_python_no_py_signatures
+@@ -1767,6 +1768,7 @@ class build_options:
+         install_prefix,
+         libdir,
+         install_destdir,
++        libtoolize,
+         scan_boost,
+         write_full_flex_fwd_h=default_write_full_flex_fwd_h,
+         build_boost_python_extensions=default_build_boost_python_extensions,
+@@ -1830,6 +1832,7 @@ class build_options:
+     print >> f, "Boost threads enabled:", self.enable_boost_threads
+     print >> f, "Enable OpenMP if possible:", self.enable_openmp_if_possible
+     print >> f, "Enable CUDA:", self.enable_cuda
++    print >> f, "Libtoolize:", self.libtoolize
+     print >> f, "Use System Libraries:", self.use_system_libs
+     print >> f, "Install Prefix:", self.install_prefix
+     print >> f, "Libdir:", self.libdir
+@@ -1974,6 +1977,10 @@ class pre_process_args:
+         default="/usr/local",
+         help="sets the prefix for the install targets. Default: /usr/local",
+         metavar="DIRECTORY")
++      parser.option(None, "--libtoolize",
++        action="store_true",
++        default=False,
++        help="build all shared libraries with libtool.")
+       parser.option(None, "--scan_boost",
+         action="store_true",
+         default=False,

diff --git a/sci-libs/cctbx/files/2012.05.08.2305/0008-Fix-to-skip-pycbf-build.patch b/sci-libs/cctbx/files/2012.05.08.2305/0008-Fix-to-skip-pycbf-build.patch
new file mode 100644
index 0000000..7aa3a39
--- /dev/null
+++ b/sci-libs/cctbx/files/2012.05.08.2305/0008-Fix-to-skip-pycbf-build.patch
@@ -0,0 +1,52 @@
+From: Radostan Riedel <raybuntu@××××××××××.com>
+Date: Tue, 7 Aug 2012 18:08:30 +0200
+Subject: Fix to skip pycbf build
+
+---
+ cctbx_sources/cbflib_adaptbx/SConscript        |    8 ++++----
+ cctbx_sources/cbflib_adaptbx/libtbx_refresh.py |   16 ++++++++--------
+ 2 files changed, 12 insertions(+), 12 deletions(-)
+
+diff --git a/cctbx_sources/cbflib_adaptbx/SConscript b/cctbx_sources/cbflib_adaptbx/SConscript
+index 334cfc2..42ab9c3 100644
+--- a/cctbx_sources/cbflib_adaptbx/SConscript
++++ b/cctbx_sources/cbflib_adaptbx/SConscript
+@@ -90,10 +90,10 @@ if (not env_etc.no_boost_python):
+     env=env_cbflib_boost_python_ext,
+     paths=env_etc.cbflib_common_includes + [env_etc.python_include])
+ 
+-  env_cbflib_boost_python_ext.SharedLibrary(
+-    target='#lib/_pycbf',
+-    source=[prefix+"/pycbf/pycbf_wrap.c"],
+-    LIBS=env_etc.cbf_lib+env_etc.libs_python+env_etc.libm)
++  #env_cbflib_boost_python_ext.SharedLibrary(
++  #  target='#lib/_pycbf',
++  #  source=[prefix+"/pycbf/pycbf_wrap.c"],
++  #  LIBS=env_etc.cbf_lib+env_etc.libs_python+env_etc.libm)
+ 
+   Export("env_cbflib_boost_python_ext")
+ 
+diff --git a/cctbx_sources/cbflib_adaptbx/libtbx_refresh.py b/cctbx_sources/cbflib_adaptbx/libtbx_refresh.py
+index 51b3e42..dd1b8e9 100644
+--- a/cctbx_sources/cbflib_adaptbx/libtbx_refresh.py
++++ b/cctbx_sources/cbflib_adaptbx/libtbx_refresh.py
+@@ -1,11 +1,11 @@
+ from libtbx.str_utils import show_string
+ import os
+ op = os.path
+-pycbf_py = self.env.under_dist(module_name="cbflib", path="pycbf/pycbf.py")
+-if (not op.isfile(pycbf_py)):
+-  raise RuntimeError("Missing file: %s" % show_string(pycbf_py))
+-target_dir = self.env.under_build(path="lib")
+-if (not op.isdir(target_dir)):
+-  os.makedirs(target_dir)
+-print "  Copying to lib: %s" % show_string(pycbf_py)
+-open(op.join(target_dir, "pycbf.py"), "w").write(open(pycbf_py).read())
++#pycbf_py = self.env.under_dist(module_name="cbflib", path="pycbf/pycbf.py")
++#if (not op.isfile(pycbf_py)):
++#  raise RuntimeError("Missing file: %s" % show_string(pycbf_py))
++#target_dir = self.env.under_build(path="lib")
++#if (not op.isdir(target_dir)):
++#  os.makedirs(target_dir)
++#print "  Copying to lib: %s" % show_string(pycbf_py)
++#open(op.join(target_dir, "pycbf.py"), "w").write(open(pycbf_py).read())

diff --git a/sci-libs/cctbx/files/2012.05.08.2305/0009-build-libann-statically.patch b/sci-libs/cctbx/files/2012.05.08.2305/0009-build-libann-statically.patch
new file mode 100644
index 0000000..77ba2b2
--- /dev/null
+++ b/sci-libs/cctbx/files/2012.05.08.2305/0009-build-libann-statically.patch
@@ -0,0 +1,27 @@
+From: Radostan Riedel <raybuntu@××××××××××.com>
+Date: Thu, 19 Jul 2012 11:29:57 +0200
+Subject: build libann statically
+
+---
+ cctbx_sources/annlib_adaptbx/SConscript |    8 +++++---
+ 1 file changed, 5 insertions(+), 3 deletions(-)
+
+diff --git a/cctbx_sources/annlib_adaptbx/SConscript b/cctbx_sources/annlib_adaptbx/SConscript
+index 31b4da6..f217b3f 100644
+--- a/cctbx_sources/annlib_adaptbx/SConscript
++++ b/cctbx_sources/annlib_adaptbx/SConscript
+@@ -29,9 +29,11 @@ if (libtbx.manual_date_stamp < 20090819):
+   env.Replace(CXXFLAGS=env_etc.cxxflags_base)
+   env.Replace(SHCXXFLAGS=env_etc.cxxflags_base)
+ 
+-if (env_etc.static_libraries): builder = env.StaticLibrary
+-else:                          builder = env.SharedLibrary
+-builder(target='#lib/ann',
++#if (env_etc.static_libraries): builder = env.StaticLibrary
++#else:                          builder = env.SharedLibrary
++# Create a static library since the changes are incompatiple
++# with debian's libann
++env.StaticLibrary(target='#lib/ann',
+   source = ["../annlib/src/ANN.cpp",
+             "../annlib/src/bd_fix_rad_search.cpp",
+             "../annlib/src/bd_pr_search.cpp",

diff --git a/sci-libs/cctbx/files/2012.05.08.2305/0010-adding-setup_py.patch b/sci-libs/cctbx/files/2012.05.08.2305/0010-adding-setup_py.patch
new file mode 100644
index 0000000..7599d82
--- /dev/null
+++ b/sci-libs/cctbx/files/2012.05.08.2305/0010-adding-setup_py.patch
@@ -0,0 +1,662 @@
+From: Baptiste Carvello <devel@×××××××××××××××××.net>
+Date: Tue, 21 Aug 2012 16:10:19 +0200
+Subject: adding-setup_py
+
+---
+ cctbx_sources/stdlib.py |    4 +
+ sconsutils.py           |  485 +++++++++++++++++++++++++++++++++++++++++++++++
+ setup.py                |  136 +++++++++++++
+ 3 files changed, 625 insertions(+)
+ create mode 100755 cctbx_sources/stdlib.py
+ create mode 100644 sconsutils.py
+ create mode 100755 setup.py
+
+diff --git a/cctbx_sources/stdlib.py b/cctbx_sources/stdlib.py
+new file mode 100755
+index 0000000..759f689
+--- /dev/null
++++ b/cctbx_sources/stdlib.py
+@@ -0,0 +1,4 @@
++from libtbx.forward_compatibility import stdlib_import
++
++math = stdlib_import("math")
++random = stdlib_import("random")
+diff --git a/sconsutils.py b/sconsutils.py
+new file mode 100644
+index 0000000..322585b
+--- /dev/null
++++ b/sconsutils.py
+@@ -0,0 +1,485 @@
++from distutils.sysconfig import get_python_lib, get_config_var
++from distutils.command.build_ext import build_ext as _build_ext
++from distutils.command.build_py import build_py as _build_py
++from distutils.command.install_lib import install_lib as _install_lib
++from distutils.command.install_data import install_data as _install_data
++from distutils.command.clean import clean as _clean
++from distutils.cmd import Command as _Command
++from distutils.dir_util import remove_tree
++from distutils.util import change_root, convert_path
++from distutils.errors import DistutilsExecError
++from distutils import log
++import sys, os
++import SCons.Script
++import libtbx
++import libtbx.env_config
++from libtbx.path import relocatable_path, absolute_path
++from libtbx.path import relpath    # don't use relpath from os.path, introduced in 2.6
++from libtbx.utils import import_python_object
++import threading
++import pickle
++
++opj = os.path.join
++configure_list = []
++scons_buildargv = []
++scons_installargv = []
++SRCDIR=''
++
++class Command(_Command):
++    def run_scons(self, argv):
++        cwd = os.getcwd()
++        builddir = opj(os.path.abspath(self.build_temp), 'cctbx-build')    # build_temp must be set by subclass
++        if not os.path.exists(builddir):
++            if not os.path.exists(os.path.abspath(self.build_temp)):
++                os.mkdir(os.path.abspath(self.build_temp))
++            os.mkdir(builddir)
++        elif not os.path.isdir(builddir):
++            raise RuntimeError(("Build directory '%s' cannot be created "
++                                "because of existing file") % builddir)
++        os.chdir(builddir)
++        if '%PREFIX%' in configure_list:
++            idx=configure_list.index('%PREFIX%')
++            configure_list[idx] = self.prefix    # prefix must be set by subclass
++        libtbx.env_config.cold_start(configure_list)
++        os.environ["LIBTBX_BUILD"] = builddir
++        os.environ['PYTHONPATH'] = ':'.join(sys.path)
++        self.spawn(argv)
++        os.chdir(cwd)
++
++class build_ext(_build_ext, Command):
++    user_options = _build_ext.user_options + [
++        ('prefix=', None, "installation prefix (default: python installation prefix")
++    ]
++    def initialize_options(self):
++        _build_ext.initialize_options(self)
++        self.prefix = None
++    def finalize_options(self):
++        _build_ext.finalize_options(self)
++        if not self.prefix:
++            self.prefix = get_config_var('prefix')    # on Debian: 'usr'
++    def run(self):
++        builddir = opj(os.path.abspath(self.build_temp), 'cctbx-build')    # build_temp set by _build_ext
++        self.run_scons(scons_buildargv)
++        for ext in self.extensions:
++            if len(ext.sources) != 1 or  ext.sources[0] != '%SCONSLIB%':
++                log.warn("Don't know how to build extension '%s' -- skipping",
++                    ext.name)
++                continue
++            dst = self.get_ext_fullpath(ext.name)
++            bld = opj(builddir, 'lib', os.path.basename(dst))
++            if os.path.isfile(bld):
++                self.copy_file(bld, dst)
++
++class build_py(_build_py):
++    def build_module (self, module, module_file, package):
++        if type(package) is str:
++            package = package.split('.')
++        elif type(package) not in (list, tuple):
++            raise TypeError, \
++                  "'package' must be a string (dot-separated), list, or tuple"
++
++        # Now put the module source file into the "build" area -- this is
++        # easy, we just copy it somewhere under self.build_lib (the build
++        # directory for Python source).
++        outfile = self.get_module_outfile(self.build_lib, package, module)
++        dir = os.path.dirname(outfile)
++        self.mkpath(dir)
++        # If the module contains non-blank, non-comment/docstring lines, and doesn't have
++        # the __future__ import, add it before the first non-comment/docstring line
++        empty = True
++        found = False
++        docstring = None
++        file_obj = open(module_file)
++        for line in file_obj:
++            if docstring:
++                if (line.count(docstring) % 2) == 1:
++                    # FIXME this logic will fail with lines such as """ + ''',
++                    # but nobody with a sane mind would do that, would they ?
++                    docstring = None
++                continue
++            if line == "from __future__ import division\n":
++                found = True
++                break
++            if line.isspace() or line.startswith('#'):
++                continue
++            if line.startswith('"""') and (line.count('"""') % 2) == 1:
++                docstring = '"""'
++                continue
++            if line.startswith('"'):
++                continue
++            if line.startswith("'''") and (line.count("'''") % 2) == 1:
++                docstring = "'''"
++                continue
++            if line.startswith("'"):
++                continue
++            empty = False
++            break
++        file_obj.close()
++        if empty or found:
++            return self.copy_file(module_file, outfile, preserve_mode=0)
++        elif self.dry_run:
++            if os.path.isdir(outfile):
++                outfile = opj(outfile, os.path.basename(module_file))
++            log.info("copying with modification %s -> %s", module_file, outfile)
++            return outfile, True
++        else:
++            if os.path.isdir(outfile):
++                outfile = opj(outfile, os.path.basename(module_file))
++            log.info("copying with modification %s -> %s", module_file, outfile)
++            file_obj = open(module_file)
++            outfile_obj = open(outfile, 'w')
++            written = False
++            docstring = None
++            for line in file_obj:
++                if not written:
++                    if docstring:
++                        if (line.count(docstring) % 2) == 1:
++                            docstring = None
++                        outfile_obj.write(line)
++                        continue
++                    if line.isspace() or line.startswith('#'):
++                        outfile_obj.write(line)
++                        continue
++                    if line.startswith('"""') and (line.count('"""') % 2) == 1:
++                        docstring = '"""'
++                        outfile_obj.write(line)
++                        continue
++                    if line.startswith('"'):
++                        outfile_obj.write(line)
++                        continue
++                    if line.startswith("'''") and (line.count("'''") % 2) == 1:
++                        docstring = "'''"
++                        outfile_obj.write(line)
++                        continue
++                    if line.startswith("'"):
++                        outfile_obj.write(line)
++                        continue
++                    outfile_obj.write("from __future__ import division\n")
++                    written = True
++                outfile_obj.write(line)
++            outfile_obj.close()
++            file_obj.close()
++            return outfile, True
++
++class test(_Command):
++    description = "runs the tests in the distutils build directory"
++    user_options = [
++        ('build-lib=', None,
++         "distutils build directory (default: 'build.build-lib')"),
++        ('build-temp=', 't',
++         "directory for temporary files (default: 'build.build-temp')")
++    ]
++    def initialize_options(self):
++        self.build_lib = None
++        self.build_temp = None
++    def finalize_options(self):
++        self.set_undefined_options('build',
++                                   ('build_lib', 'build_lib'),
++                                   ('build_temp', 'build_temp'))
++    def run(self):
++        libdir = os.path.abspath(os.path.abspath(self.build_lib))
++        builddir = opj(os.path.abspath(self.build_temp), 'cctbx-build')
++        testdir = opj(os.path.abspath(self.build_temp), 'cctbx-test')
++        self.setup_test_env(builddir, libdir, testdir)
++        os.environ["LIBTBX_BUILD"] = testdir
++        env = libtbx.env_config.unpickle()
++        os.environ['PYTHONPATH'] = ':'.join([libdir] + sys.path[5:])
++        llp = os.environ.get('LD_LIBRARY_PATH')
++        if llp is not None:
++            os.environ['LD_LIBRARY_PATH'] = ':'.join([opj(builddir, 'lib', '.libs'), llp])
++        else:
++            os.environ['LD_LIBRARY_PATH'] = opj(builddir, 'lib', '.libs')
++        os.chdir(testdir)
++        failed = []
++        for m in env.module_list:
++            for (module_name,dist_path) in m.name_and_dist_path_pairs():
++                try:
++#                    tst_list = import_python_object(
++#                            import_path="%s.run_tests.tst_list" % module_name,    Does not work yet
++#                            error_prefix="",
++#                            target_must_be="",
++#                            where_str="").object 
++                    run_func = import_python_object(
++                            import_path="%s.run_tests.run" % module_name,
++                            error_prefix="",
++                            target_must_be="",
++                            where_str="").object
++                    tst_mod = file(opj(abs(dist_path), "run_tests.py"))    # Ugly, temporary
++                    tst_lines = [l.strip() for l in tst_mod]
++                    tst_mod.close()
++                    tst_code = " ".join(["("] +
++                                        tst_lines[(tst_lines.index("tst_list = (")+1)
++                                                 :(tst_lines.index(")")+1)]
++                                        )
++                    tst_list = eval(tst_code)
++
++                except Exception:
++                    continue
++                for tst in tst_list:    # adapted from libtbx.test_utils.iter_tests_cmd
++                    cmd_args = []
++                    if (type(tst) == type([])):
++#                        cmd_args = tst[1:]    FIXME why only in quick mode?
++                        tst = tst[0]
++                    if (tst.startswith("$B")):
++                        tst_path = tst.replace("$B", builddir)
++                    else:
++                        tst_path = tst.replace("$D", abs(dist_path))
++                    if "$" in tst_path or '"' in tst_path:
++                        log.warn("Could not run test '%s':\n%s", tst, "Unexpected '$' in test path")
++                        failed.append([module_name,tst,AssertionError("Unexpected '$' in test path")])
++                        continue
++                    if '"' in tst_path:
++                        log.warn("Could not run test '%s':\n%s", tst, "Unexpected '\"' in test path")
++                        failed.append([module_name,tst,AssertionError("Unexpected '\"' in test path")])
++                        continue
++                    tst_path = os.path.normpath(tst_path)
++                    if (tst_path.endswith(".py")):
++                        cmd = [sys.executable, tst_path] + cmd_args
++                    else:
++                        cmd = [tst_path] + cmd_args
++                    try:
++                        self.spawn(cmd)
++                    except DistutilsExecError, e:
++                        log.warn("Failure in test '%s':\n%s", tst, str(e))
++                        failed.append([module_name,tst,e])
++                    except Exception, e:
++                        log.warn("Exception in test '%s':\n%s", tst, str(e))
++                        failed.append([module_name,tst,e])
++        if failed:
++            log.warn("Some tests failed:")
++            for n,t,e in failed:
++                log.warn("    module %s, test %s" % (n,t))
++            raise RuntimeError("Test failures")
++
++    def setup_test_env(self, builddir, libdir, testdir):
++        """ Create the test directory and the temporary libtbx_env pickle object """
++        if not os.path.exists(testdir):
++            if not os.path.exists(os.path.abspath(self.build_temp)):
++                os.mkdir(os.path.abspath(self.build_temp))
++            os.mkdir(testdir)
++        elif not os.path.isdir(testdir):
++            raise RuntimeError(("Test directory '%s' cannot be created "
++                                "because of existing file") % testdir)
++        os.environ["LIBTBX_BUILD"] = builddir
++        env = libtbx.env_config.unpickle()
++        module_dist_paths = {}
++        for key, value in env.module_dist_paths.items():
++            head, module = os.path.split(abs(value))
++            module_dist_paths[key] = relocatable_path(absolute_path(libdir), module)
++        env.module_dist_paths = module_dist_paths
++        for module in env.module_list:
++            paths = []
++            for path in module.dist_paths:
++                if path != None:
++                    head, tail = os.path.split(abs(path))
++                    rp = relocatable_path(absolute_path(libdir), tail)
++                    paths.append(rp)
++                else:
++                    paths.append(None)
++            module.dist_paths = paths
++        file_obj = open(opj(testdir,'libtbx_env'), 'wb')
++        pickle.dump(env, file_obj, 0)
++        file_obj.close()
++
++class install_lib(_install_lib, Command):
++    user_options = _install_lib.user_options + [
++        ('build-temp=', 't',
++         "directory for temporary files (default: 'build.build-temp')"),
++        ('prefix=', None, "installation prefix (default: 'install.prefix')"),
++        ('root=', None,
++         "install everything relative to this alternate root directory (default: 'install.root')")
++    ]
++    def initialize_options(self):
++        _install_lib.initialize_options(self)
++        self.build_temp = None
++        self.prefix = None
++        self.root = None
++    def finalize_options(self):
++        _install_lib.finalize_options(self)
++        self.set_undefined_options('build',
++                                   ('build_temp', 'build_temp'))
++        self.set_undefined_options('install',
++                                   ('prefix', 'prefix'),
++                                   ('root', 'root'))
++    def run(self):
++        _install_lib.run(self)
++        if self.root != None:
++            ip = '--install_destdir'
++            if ip not in configure_list:
++                configure_list.extend([ip, self.root])
++        self.run_scons(scons_installargv)
++
++class install_data(_install_data, Command):
++    user_options = _install_data.user_options + [
++        ('build-temp=', 't',
++         "directory for temporary files (default: 'build.build-temp')"),
++        ('prefix=', None, "installation prefix (default: 'install.prefix')")
++    ]
++    def initialize_options(self):
++        _install_data.initialize_options(self)
++        self.build_temp = None
++        self.prefix = None
++    def finalize_options(self):
++        _install_data.finalize_options(self)
++        self.set_undefined_options('build',
++                                   ('build_temp', 'build_temp'))
++        self.set_undefined_options('install',
++                                   ('prefix', 'prefix'))
++    def run(self):
++        # filter the list
++        newdf = []
++        libtbx_env_path = None
++        for f in self.data_files:
++            if type(f) is str:
++                newdf.append(f)
++                continue
++            if '%LIBTBXENV%' in f[1]:
++                f = (f[0], [p for p in f[1] if p != '%LIBTBXENV%'])
++                libtbx_env_path = opj(convert_path(f[0]), 'libtbx_env')
++                if not os.path.isabs(libtbx_env_path):    # mimic the logic in install_data
++                    libtbx_env_path = opj(self.install_dir, libtbx_env_path)
++                elif self.root:
++                    libtbx_env_path = change_root(self.root, libtbx_env_path)
++                # we leave the directory in, so that distutils will create it
++            newdf.append(f)
++        self.data_files = newdf
++        _install_data.run(self)
++        if libtbx_env_path is not None:
++            self.install_libtbx_env(libtbx_env_path)
++            self.outfiles.append(libtbx_env_path)
++
++    def install_libtbx_env(self, libtbx_env_path):
++        """ Modify libtbx_env pickle object to set the correct paths. """
++        builddir = opj(os.path.abspath(self.build_temp), 'cctbx-build')
++        os.environ["LIBTBX_BUILD"] = builddir
++        env = libtbx.env_config.unpickle()
++        env.build_path = absolute_path(self.prefix)
++        build_path = env.build_path
++        python_lib = get_python_lib()
++        rel_path = opj(python_lib, 'cctbx')
++        env.bin_path = relocatable_path(build_path, 'bin')
++        env.lib_path = relocatable_path(build_path, 'lib')
++        env.include_path = relocatable_path(build_path, 'include')
++        env.repository_paths = relocatable_path(build_path, rel_path)
++        env.scons_dist_path = None
++        env.pythonpath = None
++        env.exe_path = env.bin_path
++        env.python_exe = relocatable_path(build_path, sys.executable)
++        env.path_utility = relocatable_path(build_path,
++                opj(rel_path, 'libtbx', 'command_line', 'path_utility.py'))
++        module_dist_paths = {}
++        for key, value in env.module_dist_paths.items():
++            head, module = os.path.split(abs(value))
++            module_dist_paths[key] = relocatable_path(build_path,
++                    opj(rel_path, module))
++        env.module_dist_paths = module_dist_paths
++        for module in env.module_list:
++            paths = []
++            for path in module.dist_paths:
++                if path != None:
++                    head, tail = os.path.split(abs(path))
++                    rp = relocatable_path(build_path, opj(rel_path, tail))
++                    paths.append(rp)
++                else:
++                    paths.append(None)
++            module.dist_paths = paths
++        _dispatcher_registry={}
++        for key, value in env._dispatcher_registry.items():
++            new_key = relocatable_path(anchor=build_path,
++                                       relocatable=key.relocatable)
++            rel = relpath(abs(value), SRCDIR)
++            new_val = relocatable_path(anchor=absolute_path(rel_path),
++                                       relocatable=rel)
++            _dispatcher_registry[new_key] = new_val
++        env._dispatcher_registry = _dispatcher_registry
++        # install the environment file in the data dir
++        file_obj = open(libtbx_env_path, 'wb')
++        pickle.dump(env, file_obj, 0)
++        file_obj.close()
++
++class clean(_clean):
++    def run(self):
++        # remove the scons build dir
++        builddir = opj(os.path.abspath(self.build_temp), 'cctbx-build')
++        if os.path.exists(builddir):
++            remove_tree(builddir, dry_run=self.dry_run)
++        else:
++            log.debug("'%s' does not exist -- can't clean it",
++                      builddir)
++        # remove the scons test dir
++        testdir = opj(os.path.abspath(self.build_temp), 'cctbx-test')
++        if os.path.exists(testdir):
++            remove_tree(testdir, dry_run=self.dry_run)
++        else:
++            log.debug("'%s' does not exist -- can't clean it",
++                      testdir)
++        # call the base class to remove the distutils dirs
++        _clean.run(self)
++
++# adapted from setuptools
++# authors: Phillip J. Eby, Tarek Ziade and the distutils SIG
++# licence: PSF or ZPL
++
++from distutils.util import convert_path
++import re
++
++EXTPAT1 = re.compile(r"^from (\S+_ext) import")
++EXTPAT2 = re.compile(r"^import (\S+_ext)$")
++EXTPAT3 = re.compile(r"boost.python.import_ext\(['\"](\S+_ext)['\"]\)$")
++EXTPAT4 = re.compile(r"import_ext\(['\"](\S+_ext)['\"]\)$")    # in module boost.python!
++
++def find_packages_and_extensions(where='.', exclude=()):
++    """Return a list all Python packages found within directory 'where'
++    and a list all extensions that need to be installed inside those packages
++
++    'where' should be supplied as a "cross-platform" (i.e. URL-style) path; it
++    will be converted to the appropriate local path syntax.  'exclude' is a
++    sequence of package names to exclude; '*' can be used as a wildcard in the
++    names, such that 'foo.*' will exclude all subpackages of 'foo' (but not
++    'foo' itself).
++    """
++    out = []
++    outext = set()
++    stack=[(convert_path(where), '')]
++
++    while stack:
++
++        where,prefix = stack.pop(0)
++        for name in os.listdir(where):
++
++            fn = opj(where,name)
++            if ('.' not in name and os.path.isdir(fn) and
++                os.path.isfile(opj(fn,'__init__.py'))
++            ):
++
++                out.append(prefix+name); stack.append((fn,prefix+name+'.'))
++
++            if name.endswith('.py'):
++
++                f = open(opj(where, name))
++                for l in f:
++
++                    m = EXTPAT1.match(l)
++                    if m is not None:
++                        outext.add(m.group(1))
++
++                    m = EXTPAT2.match(l)
++                    if m is not None:
++                        outext.add(m.group(1))
++
++                    m = EXTPAT3.search(l)
++                    if m is not None:
++                        outext.add(m.group(1))
++
++                    if name == 'python.py' and prefix.endswith('boost.'):
++                        m = EXTPAT4.search(l)
++                        if m is not None:
++                            outext.add(m.group(1))
++
++                f.close()
++
++    for pat in list(exclude)+['ez_setup', 'distribute_setup']:
++        from fnmatch import fnmatchcase
++        out = [item for item in out if not fnmatchcase(item,pat)]
++
++    return out, list(outext)
+diff --git a/setup.py b/setup.py
+new file mode 100755
+index 0000000..033dc9e
+--- /dev/null
++++ b/setup.py
+@@ -0,0 +1,142 @@
++from distutils.core import setup, Extension
++import sys, os, shutil
++
++# General settings
++opj = os.path.join
++CURDIR = os.getcwd()
++SRCDIR = opj(CURDIR, 'cctbx_sources')
++py_vers = sys.version_info
++py_major = py_vers[0]
++py_minor = py_vers[1]
++py_str = 'python%s.%s'%(py_major, py_minor)
++clipper = opj('clipper_adaptbx','clipper')
++boost = opj('boost_adaptbx','boost')
++libtbx_pypath = opj('libtbx','pythonpath')
++scons_exe = '/usr/bin/scons'    # FIXME platform dependent path
++scons_path = '/usr/lib/scons/'
++PATHLIST= [ SRCDIR,
++            opj(SRCDIR, libtbx_pypath),
++            opj(SRCDIR, clipper),
++            opj(SRCDIR, boost),
++            scons_path,
++          ]
++for p in PATHLIST:
++    if p not in sys.path:
++        # we need to insert at the front, in case cctbx is already installed
++        sys.path.insert(0,p)
++
++import sconsutils
++from sconsutils import find_packages_and_extensions, build_ext, build_py, test, install_lib, install_data, clean
++
++sconsutils.SRCDIR = SRCDIR
++
++# Debian Multiarch magic
++multiarch = os.environ.get('DEB_HOST_MULTIARCH')
++libdir = os.environ.get('MULTILIBDIR')
++if multiarch == None:
++    multiarch = ''
++else:
++    libdir = 'lib/' + multiarch
++
++if libdir == None:
++    libdir = 'lib'
++# Configure settings
++# We need this directory to get env_config.cold_start to run!
++# trailing slash is important
++init_dir = opj(SRCDIR, 'libtbx')+os.sep    # the separator is needed for dirname to do the right thing
++build_opts = [ '--libtoolize',
++               '--use_system_libs',
++               '--use-environment-flags',
++               '--libdir', libdir,
++               '--install_prefix', '%PREFIX%',    # prefix will be replaced at run time
++             ]
++conf_modules = [ 'annlib_adaptbx',
++                 'boost_adaptbx',
++                 'cbflib_adaptbx',
++                 'ccp4io_adaptbx',
++                 'cctbx',
++                 'chiltbx',
++                 'clipper_adaptbx',
++                 'crys3d',
++                 'fable',
++                 'fftw3tbx',
++                 'gltbx',
++                 'iotbx',
++                 'libtbx',
++                 'mmtbx',
++                 'omptbx',
++                 'rstbx',
++                 'scitbx',
++                 'smtbx',
++                 'spotfinder',
++                 'tbxx',
++                 'tntbx',
++                 'ucif',
++                 'wxtbx',
++               ]
++sconsutils.configure_list = [init_dir]
++sconsutils.configure_list.extend(build_opts)
++sconsutils.configure_list.extend(conf_modules)
++
++# Build settings
++sconsutils.scons_buildargv = [sys.executable, scons_exe]
++
++# Install settings
++sconsutils.scons_installargv = [sys.executable, scons_exe, 'install']
++
++# Setup settings
++
++NAME = 'cctbx'
++VERSION = '2012.05.08.2305'
++DESCRIPTION = 'cctbx'
++AUTHOR = 'cctbx'
++AUTHOR_EMAIL = 'cctbx@×××××××.gov'
++URL = 'http://cctbx.sourceforge.net/'
++LICENSE = 'CCTBX 2.0'
++KEYWORDS = 'crystallography'
++SCRIPTS = []
++PKG_DATA = {}
++EXTRA_PATH = 'cctbx'
++
++MODS = ['stdlib']
++
++PACKDIR = { 'boost' : 'cctbx_sources/boost_adaptbx/boost',    # in setup, paths must stay in unix syntax
++            'clipper' : 'cctbx_sources/clipper_adaptbx/clipper',    # also, let's keep them relative
++            'optik' : 'cctbx_sources/libtbx/pythonpath/optik',    # FIXME installs incompatible fork to global path
++            'tntbx' : 'cctbx_sources/tntbx/tntbx',
++            '' : 'cctbx_sources',
++          }
++
++PACKS = []
++EXT_MODULES = []
++for key, value in PACKDIR.items():
++    p, e = find_packages_and_extensions(value)
++    PACKS.extend(p)
++    EXT_MODULES.extend(e)
++    if key != '':
++        PACKS.append(key)
++
++EXT_MODULES = [ Extension(e, ['%SCONSLIB%']) for e in EXT_MODULES ]    # special treatment from install_lib
++
++setup(name=NAME,
++      version = VERSION,
++      author = AUTHOR,
++      author_email = AUTHOR_EMAIL,
++      url = URL,
++      description = DESCRIPTION,
++      license = LICENSE,
++      keywords = KEYWORDS,
++      extra_path = EXTRA_PATH,
++      scripts = SCRIPTS,
++      py_modules = MODS,
++      package_dir = PACKDIR,
++      packages = PACKS,
++      ext_modules = EXT_MODULES,
++      data_files = [('share/cctbx/%s'%(py_str), ['%LIBTBXENV%'])],    # special treatment from install_data
++      cmdclass = {'build_ext': build_ext,
++                  'build_py': build_py,
++                  'test': test,
++                  'install_lib': install_lib,
++                  'install_data': install_data,
++                  'clean': clean},
++     )

diff --git a/sci-libs/cctbx/files/2012.05.08.2305/0011-fix-missing-python-lib-during-linking.patch b/sci-libs/cctbx/files/2012.05.08.2305/0011-fix-missing-python-lib-during-linking.patch
new file mode 100644
index 0000000..6724c0c
--- /dev/null
+++ b/sci-libs/cctbx/files/2012.05.08.2305/0011-fix-missing-python-lib-during-linking.patch
@@ -0,0 +1,47 @@
+From: Radostan Riedel <raybuntu@××××××××××.com>
+Date: Thu, 19 Jul 2012 23:26:30 +0200
+Subject: fix missing python lib during linking
+
+---
+ cctbx_sources/libtbx/SConscript              |    4 ++--
+ cctbx_sources/scitbx/boost_python/SConscript |    2 +-
+ 2 files changed, 3 insertions(+), 3 deletions(-)
+
+diff --git a/cctbx_sources/libtbx/SConscript b/cctbx_sources/libtbx/SConscript
+index 58bdd30..53e1512 100644
+--- a/cctbx_sources/libtbx/SConscript
++++ b/cctbx_sources/libtbx/SConscript
+@@ -54,9 +54,11 @@ def set_python_include_and_libs(env_etc):
+   env_etc.python_include = libtbx.env_config.python_include_path()
+   if (sys.platform == "win32"):
+     env_etc.libs_python = ["python" + sys.version[0] + sys.version[2]]
++    env_etc.py_lib = 'python%s%s'%(sys.version[0], sys.version[2])
+     env_etc.libpath_python = [sys.prefix + r"\libs"]
+   else:
+     env_etc.libs_python = []
++    env_etc.py_lib = 'python%s.%s'%(sys.version[0], sys.version[2])
+     env_etc.libpath_python = []
+   if (env_etc.compiler.startswith("darwin_")):
+     env_etc.python_framework = "/".join(
+@@ -1034,8 +1036,6 @@ def check_syslib(lib, extra_libs=None):
+     return True
+ env_etc.check_syslib = check_syslib
+ 
+-env_etc.py_lib = 'python%s.%s'%(sys.version[0], sys.version[2])
+-
+ if (libtbx.env.build_options.use_system_libs):
+   env_etc.use_system_libs = True
+ 
+diff --git a/cctbx_sources/scitbx/boost_python/SConscript b/cctbx_sources/scitbx/boost_python/SConscript
+index 1f396e5..b906eb3 100644
+--- a/cctbx_sources/scitbx/boost_python/SConscript
++++ b/cctbx_sources/scitbx/boost_python/SConscript
+@@ -7,7 +7,7 @@ env_etc.enable_more_warnings(env=env)
+ env.Append(CXXFLAGS=env_etc.cxxflags_bpl_defines_base)
+ env.Append(SHCXXFLAGS=env_etc.cxxflags_bpl_defines_base)
+ env.Append(LIBPATH=env_etc.libpath_python)
+-env.Append(LIBS=[env_etc.boost_python] + env_etc.libs_python)
++env.Append(LIBS=[env_etc.boost_python] + [env_etc.py_lib,] + env_etc.libs_python)
+ env_etc.include_registry.append(
+   env=env,
+   paths=env_etc.scitbx_common_includes + [env_etc.python_include])

diff --git a/sci-libs/cctbx/files/2012.05.08.2305/0012-fix-to-remove-cctbx.python-interpreter.patch b/sci-libs/cctbx/files/2012.05.08.2305/0012-fix-to-remove-cctbx.python-interpreter.patch
new file mode 100644
index 0000000..ec9a216
--- /dev/null
+++ b/sci-libs/cctbx/files/2012.05.08.2305/0012-fix-to-remove-cctbx.python-interpreter.patch
@@ -0,0 +1,29 @@
+From: Radostan Riedel <raybuntu@××××××××××.com>
+Date: Mon, 23 Jul 2012 23:58:46 +0200
+Subject: fix to remove cctbx.python interpreter
+
+---
+ cctbx_sources/rstbx/bpcx/uc1_2.py       |    2 +-
+ cctbx_sources/rstbx/bpcx/uc1_2_reeke.py |    2 +-
+ 2 files changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/cctbx_sources/rstbx/bpcx/uc1_2.py b/cctbx_sources/rstbx/bpcx/uc1_2.py
+index 95ee9cd..1abf8e1 100644
+--- a/cctbx_sources/rstbx/bpcx/uc1_2.py
++++ b/cctbx_sources/rstbx/bpcx/uc1_2.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env cctbx.python
++#!/usr/bin/env python
+ #
+ # Biostruct-X Data Reduction Use Case 1.2:
+ #
+diff --git a/cctbx_sources/rstbx/bpcx/uc1_2_reeke.py b/cctbx_sources/rstbx/bpcx/uc1_2_reeke.py
+index c07c015..8eebd49 100644
+--- a/cctbx_sources/rstbx/bpcx/uc1_2_reeke.py
++++ b/cctbx_sources/rstbx/bpcx/uc1_2_reeke.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env cctbx.python
++#!/usr/bin/env python
+ #
+ # Biostruct-X Data Reduction Use Case 1.2:
+ #

diff --git a/sci-libs/cctbx/files/2012.05.08.2305/0013-fix-to-support-LDFLAGS-in-use_enviroment_flags.patch b/sci-libs/cctbx/files/2012.05.08.2305/0013-fix-to-support-LDFLAGS-in-use_enviroment_flags.patch
new file mode 100644
index 0000000..8243d93
--- /dev/null
+++ b/sci-libs/cctbx/files/2012.05.08.2305/0013-fix-to-support-LDFLAGS-in-use_enviroment_flags.patch
@@ -0,0 +1,90 @@
+From: Radostan Riedel <raybuntu@××××××××××.com>
+Date: Tue, 24 Jul 2012 17:12:30 +0200
+Subject: fix to support LDFLAGS in use_enviroment_flags
+
+---
+ cctbx_sources/libtbx/SConscript    |   11 ++++++++++-
+ cctbx_sources/libtbx/env_config.py |    7 ++++++-
+ 2 files changed, 16 insertions(+), 2 deletions(-)
+
+diff --git a/cctbx_sources/libtbx/SConscript b/cctbx_sources/libtbx/SConscript
+index 53e1512..7d51d4a 100644
+--- a/cctbx_sources/libtbx/SConscript
++++ b/cctbx_sources/libtbx/SConscript
+@@ -777,11 +777,15 @@ else:
+   # user options for any compiler from the environment variables
+   # at the time of configure
+   opts = libtbx.env.build_options
++  env_etc.ldflags_base = []
+   if( opts.use_environment_flags ):
+     print "libtbx.scons: using flags from initial environment: "
+     print "              CXXFLAGS = ", opts.env_cxxflags
+     print "              CFLAGS = ", opts.env_cflags
+     print "              CPPFLAGS = ", opts.env_cppflags
++    print "              LDFLAGS = ", opts.env_ldflags
++    flg = opts.env_ldflags.split(" ")
++    env_etc.ldflags_base = flg
+     flg = opts.env_cxxflags.split(" ")
+     if( hasattr(env_etc, "cxxflags_base") ):
+       env_etc.cxxflags_base.extend(flg)
+@@ -853,6 +857,9 @@ def env_base_sync_with_env_etc():
+     SHCFLAGS=env_etc.cflags_base,
+     SHCCFLAGS=env_etc.ccflags_base,
+     SHCXXFLAGS=env_etc.cxxflags_base)
++  env_base.Prepend(LINKFLAGS=env_etc.ldflags_base)
++  env_etc.shlinkflags.extend(env_etc.ldflags_base)
++  env_etc.shlinkflags_bpl.extend(env_etc.ldflags_base)
+ env_base_sync_with_env_etc()
+ 
+ if (static_exe):
+@@ -1070,8 +1077,10 @@ def set_libtool(env):
+   # for reference. Otherwise it will be set to 0:0:0
+   env_etc.shobjsuffix_save = env['SHOBJSUFFIX']
+   env_etc.SharedLibBuilder_save = env['BUILDERS']['SharedLibrary']
++  sh_flg = list(env_etc.ldflags_base)
++  sh_flg.extend(['-rpath', env_etc.rpath])
+   env.Replace(
+-    SHLINKFLAGS='-rpath ' + env_etc.rpath,
++    SHLINKFLAGS=sh_flg,
+     SHOBJSUFFIX='.lo',
+     SHLIBSUFFIX='.la',
+   )
+diff --git a/cctbx_sources/libtbx/env_config.py b/cctbx_sources/libtbx/env_config.py
+index 3d9133e..d8fb063 100644
+--- a/cctbx_sources/libtbx/env_config.py
++++ b/cctbx_sources/libtbx/env_config.py
+@@ -1803,6 +1803,7 @@ class build_options:
+       self.env_cxxflags = ""
+       self.env_cflags = ""
+       self.env_cppflags = ""
++      self.env_ldflags = ""
+       flg = os.environ.get("CXXFLAGS")
+       if flg is not None:
+         self.env_cxxflags = flg
+@@ -1812,6 +1813,9 @@ class build_options:
+       flg = os.environ.get("CPPFLAGS")
+       if flg is not None:
+         self.env_cppflags = flg
++      flg = os.environ.get("LDFLAGS")
++      if flg is not None:
++        self.env_ldflags = flg
+ 
+   def report(self, f=None):
+     if (f is None): f = sys.stdout
+@@ -1843,6 +1847,7 @@ class build_options:
+       print >>f, "  CXXFLAGS = ", self.env_cxxflags
+       print >>f, "  CFLAGS = ", self.env_cflags
+       print >>f, "  CPPFLAGS = ", self.env_cppflags
++      print >>f, "  LDFLAGS = ", self.env_ldflags
+ 
+ class include_registry:
+ 
+@@ -2000,7 +2005,7 @@ class pre_process_args:
+         action="store_true",
+         default=False,
+         help="add compiler flags from environment variables: CXXFLAGS, CFLAGS,"
+-             " CPPFLAGS")
++             " CPPFLAGS, LDFLAGS")
+       parser.option(None, "--force_32bit",
+         action="store_true",
+         default=False,

diff --git a/sci-libs/cctbx/files/2012.05.08.2305/0014-Fix-to-append-CPPFLAGS-to-CXXFLAGS.patch b/sci-libs/cctbx/files/2012.05.08.2305/0014-Fix-to-append-CPPFLAGS-to-CXXFLAGS.patch
new file mode 100644
index 0000000..c3e357e
--- /dev/null
+++ b/sci-libs/cctbx/files/2012.05.08.2305/0014-Fix-to-append-CPPFLAGS-to-CXXFLAGS.patch
@@ -0,0 +1,21 @@
+From: Radostan Riedel <raybuntu@××××××××××.com>
+Date: Wed, 25 Jul 2012 01:44:36 +0200
+Subject: Fix to append CPPFLAGS to CXXFLAGS.
+
+---
+ cctbx_sources/libtbx/SConscript |    2 ++
+ 1 file changed, 2 insertions(+)
+
+diff --git a/cctbx_sources/libtbx/SConscript b/cctbx_sources/libtbx/SConscript
+index 7d51d4a..11a7810 100644
+--- a/cctbx_sources/libtbx/SConscript
++++ b/cctbx_sources/libtbx/SConscript
+@@ -798,6 +798,8 @@ else:
+       env_etc.ccflags_base = flg
+     flg = opts.env_cppflags.split(" ")
+     env_etc.ccflags_base.extend(flg)
++    # Need to append CPPFLAGS to cxxflags_base too!
++    env_etc.cxxflags_base.extend(flg)
+ 
+ """ ************************ Custom Builders and Emitters ********************************* """
+ 

diff --git a/sci-libs/cctbx/files/2012.05.08.2305/0016-autogenerate-pkgconfig-files.patch b/sci-libs/cctbx/files/2012.05.08.2305/0016-autogenerate-pkgconfig-files.patch
new file mode 100644
index 0000000..5646197
--- /dev/null
+++ b/sci-libs/cctbx/files/2012.05.08.2305/0016-autogenerate-pkgconfig-files.patch
@@ -0,0 +1,305 @@
+From: Radostan Riedel <raybuntu@××××××××××.com>
+Date: Mon, 6 Aug 2012 13:50:30 +0200
+Subject: autogenerate pkgconfig files
+
+---
+ cctbx_sources/cctbx/SConscript                     |    7 ++--
+ .../cctbx/sgtbx/direct_space_asu/proto/SConscript  |    5 ++-
+ cctbx_sources/iotbx/mtz/SConscript                 |    6 +++-
+ cctbx_sources/iotbx/pdb/SConscript                 |    5 ++-
+ cctbx_sources/libtbx/SConscript                    |   37 +++++++++++++++++++-
+ cctbx_sources/mmtbx/masks/SConscript               |    5 ++-
+ cctbx_sources/omptbx/SConscript                    |    5 ++-
+ cctbx_sources/rstbx/SConscript                     |    5 ++-
+ cctbx_sources/scitbx/boost_python/SConscript       |    5 ++-
+ cctbx_sources/scitbx/minpack/SConscript            |    5 ++-
+ cctbx_sources/scitbx/slatec/SConscript             |    5 ++-
+ .../smtbx/refinement/constraints/SConscript        |    5 ++-
+ cctbx_sources/spotfinder/SConscript                |    5 ++-
+ 13 files changed, 86 insertions(+), 14 deletions(-)
+
+diff --git a/cctbx_sources/cctbx/SConscript b/cctbx_sources/cctbx/SConscript
+index 6ce770c..378cb36 100644
+--- a/cctbx_sources/cctbx/SConscript
++++ b/cctbx_sources/cctbx/SConscript
+@@ -96,9 +96,12 @@ lib_cctbx_sources = [
+ ]
+ if (env_etc.static_libraries): builder = envlm.StaticLibrary
+ else:                          builder = envlm.SharedLibrary
++name='cctbx'
+ builder(
+-  target="#lib/cctbx",
+-  source=lib_cctbx_sources)
++        target="#lib/"+name,
++        source=lib_cctbx_sources)
++desc='Library for general crystallographic applications'
++env_etc.create_pc_file(name=name, version='0.0.0', desc=desc)
+ 
+ SConscript("examples/SConscript")
+ 
+diff --git a/cctbx_sources/cctbx/sgtbx/direct_space_asu/proto/SConscript b/cctbx_sources/cctbx/sgtbx/direct_space_asu/proto/SConscript
+index 5a5cfbd..4328794 100644
+--- a/cctbx_sources/cctbx/sgtbx/direct_space_asu/proto/SConscript
++++ b/cctbx_sources/cctbx/sgtbx/direct_space_asu/proto/SConscript
+@@ -16,9 +16,12 @@ lib_asu_sources = [
+ if (env_etc.static_libraries): builder = env.StaticLibrary
+ else:                          builder = env.SharedLibrary
+ 
++name='cctbx_sgtbx_asu'
+ builder(
+-  target="#lib/cctbx_sgtbx_asu",
++  target="#lib/"+name,
+   source=lib_asu_sources)
++desc='Direct space asymmetric unit class library'
++env_etc.create_pc_file(name=name, version='0.0.0', desc=desc)
+ 
+ env = env.Clone()
+ env.Prepend(LIBS=["cctbx_sgtbx_asu"])
+diff --git a/cctbx_sources/iotbx/mtz/SConscript b/cctbx_sources/iotbx/mtz/SConscript
+index cd539e6..f7d22b8 100644
+--- a/cctbx_sources/iotbx/mtz/SConscript
++++ b/cctbx_sources/iotbx/mtz/SConscript
+@@ -9,13 +9,17 @@ env.Append(SHCXXFLAGS=env_etc.ccp4io_defines)
+ env_etc.enable_more_warnings(env=env)
+ if (env_etc.static_libraries): builder = env.StaticLibrary
+ else:                          builder = env.SharedLibrary
++name='iotbx_mtz'
+ builder(
+-  target="#lib/iotbx_mtz",
++  target="#lib/"+name,
+   source=[
+     "object.cpp",
+     "crystal.cpp",
+     "dataset.cpp",
+     "column.cpp"])
++desc='Wrapper Library to work with CCP4 MTZ files'
++env_etc.create_pc_file(name=name, version='0.0.0', desc=desc)
++
+ 
+ if (not env_etc.no_boost_python):
+   Import("env_iotbx_boost_python_ext")
+diff --git a/cctbx_sources/iotbx/pdb/SConscript b/cctbx_sources/iotbx/pdb/SConscript
+index 9b89fe1..8a83058 100644
+--- a/cctbx_sources/iotbx/pdb/SConscript
++++ b/cctbx_sources/iotbx/pdb/SConscript
+@@ -9,8 +9,9 @@ env_etc.include_registry.append(
+   paths=env_etc.iotbx_common_includes)
+ if (env_etc.static_libraries): builder = env.StaticLibrary
+ else:                          builder = env.SharedLibrary
++name='iotbx_pdb'
+ builder(
+-  target="#lib/iotbx_pdb",
++  target="#lib/"+name,
+   source=[
+     "hybrid_36_c.c",
+     "hybrid_36_cpp.cpp",
+@@ -25,6 +26,8 @@ builder(
+     "atom_selection.cpp",
+     "input.cpp",
+     "input_write.cpp"])
++desc='Fast comprehensive PDB handling library'
++env_etc.create_pc_file(name=name, version='0.0.0', desc=desc)
+ 
+ env = env.Clone()
+ env_etc.include_registry.append(env=env, paths=[env_etc.fable_include])
+diff --git a/cctbx_sources/libtbx/SConscript b/cctbx_sources/libtbx/SConscript
+index 11a7810..1e91202 100644
+--- a/cctbx_sources/libtbx/SConscript
++++ b/cctbx_sources/libtbx/SConscript
+@@ -1070,8 +1070,34 @@ env_etc.install_path = os.path.abspath(env_etc.destdir + '/' + env_etc.prefix)
+ env_etc.binpath = os.path.join(env_etc.install_path, 'bin')
+ env_etc.libpath = os.path.abspath(env_etc.install_path + '/' + env_etc.libdir)
+ env_etc.inclpath = os.path.join(env_etc.install_path, 'include')
++env_etc.pkgpath = os.path.join(env_etc.install_path, 'lib/pkgconfig')
+ env_etc.rpath = os.path.abspath(env_etc.prefix + '/' + env_etc.libdir)
+ 
++def create_pc_file(name, version, desc, requires=None, requires_private=None,
++                   conflicts=None, libs_private=None):
++  """ Create pkg-config file. """
++  fpath = '%s/%s.pc'%(abs(libtbx.env.lib_path), name)
++  pc = open(fpath, 'w')
++  pc.write('prefix=%s\n'%env_etc.prefix)
++  pc.write('exec_prefix=${PREFIX}\n')
++  pc.write('libdir=${PREFIX}/%s\n'%env_etc.libdir)
++  pc.write('includedir=${PREFIX}/include\n\n')
++  pc.write('Name: %s\n'%name)
++  pc.write('Description: %s\n'%desc)
++  pc.write('Version: %s\n'%version)
++  if requires != None:
++    pc.write('Requires: %s\n'%requires)
++  if requires_private != None:
++    pc.write('Requires.private: %s\n'%requires_private)
++  if conflicts != None:
++    pc.write('Conflicts: %s\n'%conflicts)
++  pc.write('Libs: -L${libdir} -l%s\n'%name)
++  if libs_private != None:
++    pc.write('Libs.private: %s\n'%libs_private)
++  pc.write('Cflags: -I${includedir}')
++  pc.close()
++env_etc.create_pc_file = create_pc_file
++
+ def set_libtool(env):
+   # Versioning can be provided by appending "-version-info 3:12:1" to SHLINKFLAGS
+   # Please see:
+@@ -1197,6 +1223,11 @@ def create_install_targets():
+           src = os.path.join(src_dir, root, filename)
+           env_base.Install(dest, src)
+           env_base.Alias("install-header", dest)
++        if re.match('^.*\.pc$', filename, flags=re.IGNORECASE):
++          dest = os.path.join(env_etc.pkgpath, root)
++          src = os.path.join(src_dir, root, filename)
++          env_base.Install(dest, src)
++          env_base.Alias("install-pkgconfig", dest)
+       if src_dir == lib_dir:
+         break
+ 
+@@ -1204,7 +1235,11 @@ def create_install_targets():
+   dest = env_etc.binpath
+   env_base.Install(dest, Glob('%s/*'%(exe_dev)))
+   env_base.Alias("install-bin", dest)
+-  Alias('install', ['install-header', 'install-shlib', 'install-bin'])
++  Alias('install', ['install-header',
++                    'install-shlib',
++                    'install-bin',
++                    'install-pkgconfig',
++                   ])
+   os.chdir(cwd)
+ 
+ if 'install' in COMMAND_LINE_TARGETS:
+diff --git a/cctbx_sources/mmtbx/masks/SConscript b/cctbx_sources/mmtbx/masks/SConscript
+index ef93088..a6187cc 100644
+--- a/cctbx_sources/mmtbx/masks/SConscript
++++ b/cctbx_sources/mmtbx/masks/SConscript
+@@ -13,9 +13,12 @@ lib_sources = [
+ if (env_etc.static_libraries): builder = env.StaticLibrary
+ else:                          builder = env.SharedLibrary
+ 
++name='mmtbx_masks'
+ builder(
+-  target="#lib/mmtbx_masks",
++  target="#lib/"+name,
+   source=lib_sources)
++desc='Masks for bulk solvent modelling'
++env_etc.create_pc_file(name=name, version='0.0.0', desc=desc)
+ 
+ env = env.Clone()
+ env.Prepend(LIBS=["mmtbx_masks", "iotbx_pdb"])
+diff --git a/cctbx_sources/omptbx/SConscript b/cctbx_sources/omptbx/SConscript
+index 43aac91..76bb923 100644
+--- a/cctbx_sources/omptbx/SConscript
++++ b/cctbx_sources/omptbx/SConscript
+@@ -12,9 +12,12 @@ env_etc.include_registry.append(
+   paths=[env_etc.omptbx_include])
+ if (env_etc.static_libraries): builder = env.StaticLibrary
+ else:                          builder = env.SharedLibrary
++name='omptbx'
+ builder(
+-  target="#lib/omptbx",
++  target="#lib/"+name,
+   source=["stubs.cpp"])
++desc='OpenMP interface for CCTBX'
++env_etc.create_pc_file(name=name, version='0.0.0', desc=desc)
+ 
+ if (not env_etc.no_boost_python):
+   Import("env_boost_python_ext")
+diff --git a/cctbx_sources/rstbx/SConscript b/cctbx_sources/rstbx/SConscript
+index e2958a1..6d66476 100644
+--- a/cctbx_sources/rstbx/SConscript
++++ b/cctbx_sources/rstbx/SConscript
+@@ -26,14 +26,17 @@ env_etc.include_registry.append(
+   paths=env_etc.rstbx_common_includes)
+ if (env_etc.static_libraries): builder = env.StaticLibrary
+ else:                          builder = env.SharedLibrary
++name='rstbx'
+ builder(
+-  target="#lib/rstbx",
++  target="#lib/"+name,
+   source=["dps_core/dps_core.cpp",
+           "dps_core/directional_fft.cpp",
+           "dps_core/direction.cpp",
+           "diffraction/ewald_sphere.cpp",
+           "diffraction/partial_spot_position_partial_H.cpp"
+   ])
++desc='Library for calculations in reciprocal space'
++env_etc.create_pc_file(name=name, version='0.0.0', desc=desc)
+ 
+ if (not env_etc.no_boost_python):
+   Import("env_boost_python_ext")
+diff --git a/cctbx_sources/scitbx/boost_python/SConscript b/cctbx_sources/scitbx/boost_python/SConscript
+index b906eb3..0b81d9a 100644
+--- a/cctbx_sources/scitbx/boost_python/SConscript
++++ b/cctbx_sources/scitbx/boost_python/SConscript
+@@ -19,6 +19,9 @@ lib_scitbx_boost_python_sources = [
+ ]
+ if (env_etc.static_libraries): builder = env.StaticLibrary
+ else:                          builder = env.SharedLibrary
++name=env_etc.scitbx_boost_python
+ builder(
+-  target="#lib/%s"%env_etc.scitbx_boost_python,
++  target="#lib/"+name,
+   source=lib_scitbx_boost_python_sources)
++desc='#TODO'
++env_etc.create_pc_file(name=name, version='0.0.0', desc=desc)
+diff --git a/cctbx_sources/scitbx/minpack/SConscript b/cctbx_sources/scitbx/minpack/SConscript
+index 7c325cb..ee7509e 100644
+--- a/cctbx_sources/scitbx/minpack/SConscript
++++ b/cctbx_sources/scitbx/minpack/SConscript
+@@ -9,7 +9,10 @@ env_etc.include_registry.append(
+ env.Append(LIBS=env_etc.libm)
+ if (env_etc.static_libraries): builder = env.StaticLibrary
+ else:                          builder = env.SharedLibrary
+-builder(target='#lib/scitbx_minpack', source=["raw.cpp"])
++name='scitbx_minpack'
++builder(target='#lib/'+name, source=["raw.cpp"])
++desc='C++ port of files in MINPACK'
++env_etc.create_pc_file(name=name, version='0.0.0', desc=desc)
+ 
+ if (not env_etc.no_boost_python):
+   Import("env_scitbx_boost_python_ext")
+diff --git a/cctbx_sources/scitbx/slatec/SConscript b/cctbx_sources/scitbx/slatec/SConscript
+index ca9b6da..39e38e1 100644
+--- a/cctbx_sources/scitbx/slatec/SConscript
++++ b/cctbx_sources/scitbx/slatec/SConscript
+@@ -6,4 +6,7 @@ env_etc.enable_more_warnings(env=env)
+ env.Append(LIBS=env_etc.libm)
+ if (env_etc.static_libraries): builder = env.StaticLibrary
+ else:                          builder = env.SharedLibrary
+-builder(target='#lib/scitbx_slatec', source=["lib_c.c"])
++name='scitbx_slatec'
++builder(target='#lib/'+name, source=["lib_c.c"])
++desc='C port of files in SLATEC'
++env_etc.create_pc_file(name=name, version='0.0.0', desc=desc)
+diff --git a/cctbx_sources/smtbx/refinement/constraints/SConscript b/cctbx_sources/smtbx/refinement/constraints/SConscript
+index 67d99dc..306d1a4 100644
+--- a/cctbx_sources/smtbx/refinement/constraints/SConscript
++++ b/cctbx_sources/smtbx/refinement/constraints/SConscript
+@@ -4,7 +4,10 @@ env_etc.include_registry.append(env=env,
+                                 paths=["."] + env_etc.smtbx_common_includes)
+ if (env_etc.static_libraries): builder = env.StaticLibrary
+ else:                          builder = env.SharedLibrary
+-builder(target="#lib/smtbx_refinement_constraints", source=Glob("*.cpp"))
++name='smtbx_refinement_constraints'
++builder(target="#lib/"+name, source=Glob("*.cpp"))
++desc='Library for small molecule crystallography constraints'
++env_etc.create_pc_file(name=name, version='0.0.0', desc=desc)
+ 
+ env_program = env.Clone()
+ env_program.Prepend(LIBS=[ "cctbx", "smtbx_refinement_constraints" ])
+diff --git a/cctbx_sources/spotfinder/SConscript b/cctbx_sources/spotfinder/SConscript
+index 1d73677..a63c6d9 100644
+--- a/cctbx_sources/spotfinder/SConscript
++++ b/cctbx_sources/spotfinder/SConscript
+@@ -46,9 +46,12 @@ lib_spotfinder_sources = [
+ 
+ if (env_etc.static_libraries): builder = envlm.StaticLibrary
+ else:                          builder = envlm.SharedLibrary
++name='spotfinder'
+ builder(
+-    target="#lib/spotfinder",
++    target="#lib/"+name,
+     source=lib_spotfinder_sources)
++desc='Library for locating Bragg-Spots on x-ray diffraction images'
++env_etc.create_pc_file(name=name, version='0.0.0', desc=desc)
+ 
+ if (not env_etc.no_boost_python):
+   Import("env_no_includes_boost_python_ext")

diff --git a/sci-libs/cctbx/files/2012.05.08.2305/0017-Fix-to-use-systems-include-path.patch b/sci-libs/cctbx/files/2012.05.08.2305/0017-Fix-to-use-systems-include-path.patch
new file mode 100644
index 0000000..4affc54
--- /dev/null
+++ b/sci-libs/cctbx/files/2012.05.08.2305/0017-Fix-to-use-systems-include-path.patch
@@ -0,0 +1,128 @@
+From: Radostan Riedel <raybuntu@××××××××××.com>
+Date: Tue, 7 Aug 2012 18:15:43 +0200
+Subject: Fix to use systems include path
+
+---
+ .../cbflib_adaptbx/detectors/boost_python/cbf_binary_adaptor.h   |    4 ++--
+ .../cbflib_adaptbx/detectors/boost_python/general_cbf_write.h    |    4 ++--
+ cctbx_sources/cbflib_adaptbx/detectors/cbf_adaptor.h             |    4 ++--
+ .../cbflib_adaptbx/detectors/cbf_byte_offset_optimized.cpp       |    6 +++---
+ cctbx_sources/cbflib_adaptbx/detectors/tst_memory.cpp            |    4 ++--
+ cctbx_sources/ccp4io_adaptbx/ext.cpp                             |    2 +-
+ cctbx_sources/iotbx/mtz/ext.cpp                                  |    2 +-
+ cctbx_sources/iotbx/mtz/object.h                                 |    6 +++---
+ 8 files changed, 16 insertions(+), 16 deletions(-)
+
+diff --git a/cctbx_sources/cbflib_adaptbx/detectors/boost_python/cbf_binary_adaptor.h b/cctbx_sources/cbflib_adaptbx/detectors/boost_python/cbf_binary_adaptor.h
+index 66677bd..516b319 100644
+--- a/cctbx_sources/cbflib_adaptbx/detectors/boost_python/cbf_binary_adaptor.h
++++ b/cctbx_sources/cbflib_adaptbx/detectors/boost_python/cbf_binary_adaptor.h
+@@ -3,8 +3,8 @@
+ #include <cbflib_adaptbx/detectors/cbf_adaptor.h>
+ #include <cbflib_adaptbx/detectors/cbf_byte_offset_optimized.h>
+ #include <cbflib_adaptbx/detectors/buffer_based_service.h>
+-#include <include/cbf_binary.h>
+-#include <include/cbf_compress.h>
++#include <cbf/cbf_binary.h>
++#include <cbf/cbf_compress.h>
+ 
+ namespace iotbx {
+   namespace detectors {
+diff --git a/cctbx_sources/cbflib_adaptbx/detectors/boost_python/general_cbf_write.h b/cctbx_sources/cbflib_adaptbx/detectors/boost_python/general_cbf_write.h
+index c6c1afb..f45b4d1 100644
+--- a/cctbx_sources/cbflib_adaptbx/detectors/boost_python/general_cbf_write.h
++++ b/cctbx_sources/cbflib_adaptbx/detectors/boost_python/general_cbf_write.h
+@@ -1,8 +1,8 @@
+ #ifndef GENERAL_CBF_WRITE_H
+ #define GENERAL_CBF_WRITE_H
+ #include <cbflib_adaptbx/detectors/cbf_adaptor.h>
+-#include "cbf_binary.h"
+-#include "cbf_compress.h"
++#include "cbf/cbf_binary.h"
++#include "cbf/cbf_compress.h"
+ 
+ namespace iotbx {
+   namespace detectors {
+diff --git a/cctbx_sources/cbflib_adaptbx/detectors/cbf_adaptor.h b/cctbx_sources/cbflib_adaptbx/detectors/cbf_adaptor.h
+index b5cc407..3787c7b 100644
+--- a/cctbx_sources/cbflib_adaptbx/detectors/cbf_adaptor.h
++++ b/cctbx_sources/cbflib_adaptbx/detectors/cbf_adaptor.h
+@@ -8,8 +8,8 @@
+ #include <exception>
+ #include <scitbx/array_family/flex_types.h>
+ #include <scitbx/array_family/versa_matrix.h>
+-#include <include/cbf.h>
+-#include <include/cbf_simple.h>
++#include <cbf/cbf.h>
++#include <cbf/cbf_simple.h>
+ #include <cbflib_adaptbx/detectors/basic.h>
+ 
+ #undef cbf_failnez
+diff --git a/cctbx_sources/cbflib_adaptbx/detectors/cbf_byte_offset_optimized.cpp b/cctbx_sources/cbflib_adaptbx/detectors/cbf_byte_offset_optimized.cpp
+index 2edbfb5..526556f 100644
+--- a/cctbx_sources/cbflib_adaptbx/detectors/cbf_byte_offset_optimized.cpp
++++ b/cctbx_sources/cbflib_adaptbx/detectors/cbf_byte_offset_optimized.cpp
+@@ -244,9 +244,9 @@ extern "C" {
+ #include <limits.h>
+ #include <ctype.h>
+ 
+-#include "cbf.h"
+-#include "cbf_file.h"
+-#include "cbf_byte_offset.h"
++#include "cbf/cbf.h"
++#include "cbf/cbf_file.h"
++#include "cbf/cbf_byte_offset.h"
+ #include <cbflib_adaptbx/detectors/cbf_byte_offset_optimized.h>
+ 
+ /* Changes made in the byte-offset algorithm
+diff --git a/cctbx_sources/cbflib_adaptbx/detectors/tst_memory.cpp b/cctbx_sources/cbflib_adaptbx/detectors/tst_memory.cpp
+index 5f5d9b1..d121530 100644
+--- a/cctbx_sources/cbflib_adaptbx/detectors/tst_memory.cpp
++++ b/cctbx_sources/cbflib_adaptbx/detectors/tst_memory.cpp
+@@ -1,5 +1,5 @@
+-#include <include/cbf.h>
+-#include <include/cbf_simple.h>
++#include <cbf/cbf.h>
++#include <cbf/cbf_simple.h>
+ #include <cstdio>
+ #include <string>
+ #include <exception>
+diff --git a/cctbx_sources/ccp4io_adaptbx/ext.cpp b/cctbx_sources/ccp4io_adaptbx/ext.cpp
+index ce21568..e507515 100644
+--- a/cctbx_sources/ccp4io_adaptbx/ext.cpp
++++ b/cctbx_sources/ccp4io_adaptbx/ext.cpp
+@@ -1,5 +1,5 @@
+ #include <boost/python.hpp>
+-#include <mmdb_manager.h>
++#include <mmdb/mmdb_manager.h>
+ #include <ssm_align.h>
+ 
+ namespace ccp4io_adaptbx { namespace boost_python {
+diff --git a/cctbx_sources/iotbx/mtz/ext.cpp b/cctbx_sources/iotbx/mtz/ext.cpp
+index b1a0db7..6aa416a 100644
+--- a/cctbx_sources/iotbx/mtz/ext.cpp
++++ b/cctbx_sources/iotbx/mtz/ext.cpp
+@@ -1,5 +1,5 @@
+ #include <boost/python/module.hpp>
+-#include <ccp4_errno.h>
++#include <ccp4/ccp4_errno.h>
+ 
+ namespace iotbx { namespace mtz { namespace boost_python {
+ 
+diff --git a/cctbx_sources/iotbx/mtz/object.h b/cctbx_sources/iotbx/mtz/object.h
+index da35fcf..b593534 100644
+--- a/cctbx_sources/iotbx/mtz/object.h
++++ b/cctbx_sources/iotbx/mtz/object.h
+@@ -6,9 +6,9 @@
+ # include <math.h>
+ #endif
+ 
+-#include <cmtzlib.h>
+-#include <ccp4_array.h>
+-#include <ccp4_errno.h>
++#include <ccp4/cmtzlib.h>
++#include <ccp4/ccp4_array.h>
++#include <ccp4/ccp4_errno.h>
+ #include <cctbx/sgtbx/space_group.h>
+ #include <cctbx/hendrickson_lattman.h>
+ #include <boost/shared_ptr.hpp>

diff --git a/sci-libs/cctbx/files/2012.05.08.2305/0018-Fix-to-skip-build-of-clipper-examples.patch b/sci-libs/cctbx/files/2012.05.08.2305/0018-Fix-to-skip-build-of-clipper-examples.patch
new file mode 100644
index 0000000..ffd4ebb
--- /dev/null
+++ b/sci-libs/cctbx/files/2012.05.08.2305/0018-Fix-to-skip-build-of-clipper-examples.patch
@@ -0,0 +1,52 @@
+From: Radostan Riedel <raybuntu@××××××××××.com>
+Date: Tue, 7 Aug 2012 18:19:02 +0200
+Subject: Fix to skip build of clipper examples
+
+---
+ cctbx_sources/clipper_adaptbx/SConscript |   33 +++++++++++++++---------------
+ 1 file changed, 17 insertions(+), 16 deletions(-)
+
+diff --git a/cctbx_sources/clipper_adaptbx/SConscript b/cctbx_sources/clipper_adaptbx/SConscript
+index c39047f..b0699ad 100644
+--- a/cctbx_sources/clipper_adaptbx/SConscript
++++ b/cctbx_sources/clipper_adaptbx/SConscript
+@@ -61,22 +61,23 @@ else:
+ env_exe = env.Clone()
+ env_exe.Prepend(LIBS=[env_etc.clipper_libs[0]])
+ 
+-exe = env_exe.Program(
+-  target='#exe_dev/'+env["PROGPREFIX"]+'clipper.symtest'
+-                    +env["PROGSUFFIX"],
+-  source = ["../clipper/examples/symtest.cpp",
+-           ])
+-libtbx.env.write_dispatcher_in_bin(
+-  source_file=exe[0].get_abspath(),
+-  target_file="clipper.symtest")
+-exe = env_exe.Program(
+-  target='#exe_dev/'+env["PROGPREFIX"]+'clipper.sanity_check'
+-                    +env["PROGSUFFIX"],
+-  source = ["sanity_check.cpp",
+-           ])
+-libtbx.env.write_dispatcher_in_bin(
+-  source_file=exe[0].get_abspath(),
+-  target_file="clipper.sanity_check")
++# Skip building clipper examples in Debian
++#exe = env_exe.Program(
++#  target='#exe_dev/'+env["PROGPREFIX"]+'clipper.symtest'
++#                    +env["PROGSUFFIX"],
++#  source = ["../clipper/examples/symtest.cpp",
++#           ])
++#libtbx.env.write_dispatcher_in_bin(
++#  source_file=exe[0].get_abspath(),
++#  target_file="clipper.symtest")
++#exe = env_exe.Program(
++#  target='#exe_dev/'+env["PROGPREFIX"]+'clipper.sanity_check'
++#                    +env["PROGSUFFIX"],
++#  source = ["sanity_check.cpp",
++#           ])
++#libtbx.env.write_dispatcher_in_bin(
++#  source_file=exe[0].get_abspath(),
++#  target_file="clipper.sanity_check")
+ 
+ if (hasattr(env_etc, "cctbx_include")):
+   if (not env_etc.no_boost_python):

diff --git a/sci-libs/cctbx/files/2012.05.08.2305/0101-system-cbf.patch b/sci-libs/cctbx/files/2012.05.08.2305/0101-system-cbf.patch
new file mode 100644
index 0000000..1688026
--- /dev/null
+++ b/sci-libs/cctbx/files/2012.05.08.2305/0101-system-cbf.patch
@@ -0,0 +1,16 @@
+ cctbx_sources/cbflib_adaptbx/detectors/cbf_byte_offset_optimized.h | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/cctbx_sources/cbflib_adaptbx/detectors/cbf_byte_offset_optimized.h b/cctbx_sources/cbflib_adaptbx/detectors/cbf_byte_offset_optimized.h
+index 0089325..02234d1 100644
+--- a/cctbx_sources/cbflib_adaptbx/detectors/cbf_byte_offset_optimized.h
++++ b/cctbx_sources/cbflib_adaptbx/detectors/cbf_byte_offset_optimized.h
+@@ -5,7 +5,7 @@
+ extern "C" {
+ #endif
+ #include <stdio.h>
+-#include <include/cbf_file.h>
++#include <cbf/cbf_file.h>
+ 
+   /* Decompress an array with the byte-offset algorithm */
+ 

diff --git a/sci-libs/cctbx/files/2012.05.08.2305/0101-system-clipper.patch b/sci-libs/cctbx/files/2012.05.08.2305/0101-system-clipper.patch
new file mode 100644
index 0000000..6f50e5f
--- /dev/null
+++ b/sci-libs/cctbx/files/2012.05.08.2305/0101-system-clipper.patch
@@ -0,0 +1,185 @@
+ cctbx_sources/clipper/clipper/cctbx/clipper_cctbx.h        |  2 +-
+ cctbx_sources/clipper/clipper/contrib/Makefile.dep         | 14 +++++++-------
+ cctbx_sources/clipper/clipper/contrib/edcalc.cpp           |  2 +-
+ cctbx_sources/clipper/clipper/contrib/fffear.cpp           |  2 +-
+ .../clipper/clipper/contrib/function_object_bases.h        |  6 +++---
+ cctbx_sources/clipper/clipper/contrib/sfcalc.cpp           |  2 +-
+ cctbx_sources/clipper/clipper/contrib/sfcalc_obs.cpp       |  4 ++--
+ cctbx_sources/clipper/clipper/contrib/sfweight.cpp         |  4 ++--
+ cctbx_sources/clipper/clipper/contrib/skeleton.cpp         |  2 +-
+ cctbx_sources/clipper_adaptbx/clipper/SConscript           |  1 -
+ 10 files changed, 19 insertions(+), 20 deletions(-)
+
+diff --git a/cctbx_sources/clipper/clipper/cctbx/clipper_cctbx.h b/cctbx_sources/clipper/clipper/cctbx/clipper_cctbx.h
+index bd9f7d2..079958d 100644
+--- a/cctbx_sources/clipper/clipper/cctbx/clipper_cctbx.h
++++ b/cctbx_sources/clipper/clipper/cctbx/clipper_cctbx.h
+@@ -47,7 +47,7 @@
+ #define CLIPPER_CCTBX
+ 
+ 
+-#include "../core/hkl_datatypes.h"
++#include "clipper/core/hkl_datatypes.h"
+ 
+ #include <cctbx/sgtbx/space_group.h>
+ #include <cctbx/hendrickson_lattman.h>
+diff --git a/cctbx_sources/clipper/clipper/contrib/Makefile.dep b/cctbx_sources/clipper/clipper/contrib/Makefile.dep
+index 98251b1..0fe7bb3 100644
+--- a/cctbx_sources/clipper/clipper/contrib/Makefile.dep
++++ b/cctbx_sources/clipper/clipper/contrib/Makefile.dep
+@@ -1,27 +1,27 @@
+ 
+-function_object_bases.h:	../core/hkl_datatypes.h ../core/xmap.h ../core/nxmap_operator.h 
++function_object_bases.h:	clipper/core/hkl_datatypes.h clipper/core/xmap.h clipper/core/nxmap_operator.h 
+ 
+ function_object_bases.o:	function_object_bases.cpp function_object_bases.h 
+ 
+ sfcalc.h:               	function_object_bases.h 
+ 
+-sfcalc.o:               	sfcalc.cpp sfcalc.h ../core/atomsf.h 
++sfcalc.o:               	sfcalc.cpp sfcalc.h clipper/core/atomsf.h 
+ 
+ edcalc.h:               	function_object_bases.h 
+ 
+-edcalc.o:               	edcalc.cpp edcalc.h ../core/atomsf.h 
++edcalc.o:               	edcalc.cpp edcalc.h clipper/core/atomsf.h 
+ 
+ sfcalc_obs.h:           	function_object_bases.h 
+ 
+-sfcalc_obs.o:           	sfcalc_obs.cpp sfcalc_obs.h edcalc.h ../core/hkl_compute.h ../core/resol_targetfn.h 
++sfcalc_obs.o:           	sfcalc_obs.cpp sfcalc_obs.h edcalc.h clipper/core/hkl_compute.h clipper/core/resol_targetfn.h 
+ 
+ sfweight.h:             	function_object_bases.h 
+ 
+-sfweight.o:             	sfweight.cpp sfweight.h ../core/hkl_operators.h ../core/resol_targetfn.h 
++sfweight.o:             	sfweight.cpp sfweight.h clipper/core/hkl_operators.h clipper/core/resol_targetfn.h 
+ 
+ fffear.h:               	function_object_bases.h 
+ 
+-fffear.o:               	fffear.cpp fffear.h ../core/map_interp.h 
++fffear.o:               	fffear.cpp fffear.h clipper/core/map_interp.h 
+ 
+ mapfilter.h:            	function_object_bases.h 
+ 
+@@ -29,7 +29,7 @@ mapfilter.o:            	mapfilter.cpp mapfilter.h
+ 
+ skeleton.h:             	function_object_bases.h 
+ 
+-skeleton.o:             	skeleton.cpp skeleton.h ../core/map_utils.h 
++skeleton.o:             	skeleton.cpp skeleton.h clipper/core/map_utils.h 
+ 
+ originmatch.h:          	function_object_bases.h 
+ 
+diff --git a/cctbx_sources/clipper/clipper/contrib/edcalc.cpp b/cctbx_sources/clipper/clipper/contrib/edcalc.cpp
+index f5df7b2..cc031bc 100644
+--- a/cctbx_sources/clipper/clipper/contrib/edcalc.cpp
++++ b/cctbx_sources/clipper/clipper/contrib/edcalc.cpp
+@@ -43,7 +43,7 @@
+ 
+ #include "edcalc.h"
+ 
+-#include "../core/atomsf.h"
++#include "clipper/core/atomsf.h"
+ 
+ 
+ namespace clipper {
+diff --git a/cctbx_sources/clipper/clipper/contrib/fffear.cpp b/cctbx_sources/clipper/clipper/contrib/fffear.cpp
+index 9a728f7..189855a 100644
+--- a/cctbx_sources/clipper/clipper/contrib/fffear.cpp
++++ b/cctbx_sources/clipper/clipper/contrib/fffear.cpp
+@@ -42,7 +42,7 @@
+ 
+ #include "fffear.h"
+ 
+-#include "../core/map_interp.h"
++#include "clipper/core/map_interp.h"
+ 
+ 
+ namespace clipper {
+diff --git a/cctbx_sources/clipper/clipper/contrib/function_object_bases.h b/cctbx_sources/clipper/clipper/contrib/function_object_bases.h
+index e6c98c7..4a40c73 100644
+--- a/cctbx_sources/clipper/clipper/contrib/function_object_bases.h
++++ b/cctbx_sources/clipper/clipper/contrib/function_object_bases.h
+@@ -48,9 +48,9 @@
+ #define CLIPPER_FUNCTION_OBJECT_BASES
+ 
+ 
+-#include "../core/hkl_datatypes.h"
+-#include "../core/xmap.h"
+-#include "../core/nxmap_operator.h"
++#include "clipper/core/hkl_datatypes.h"
++#include "clipper/core/xmap.h"
++#include "clipper/core/nxmap_operator.h"
+ 
+ 
+ namespace clipper {
+diff --git a/cctbx_sources/clipper/clipper/contrib/sfcalc.cpp b/cctbx_sources/clipper/clipper/contrib/sfcalc.cpp
+index 48c0d9c..a3c63f0 100644
+--- a/cctbx_sources/clipper/clipper/contrib/sfcalc.cpp
++++ b/cctbx_sources/clipper/clipper/contrib/sfcalc.cpp
+@@ -43,7 +43,7 @@
+ 
+ #include "sfcalc.h"
+ 
+-#include "../core/atomsf.h"
++#include "clipper/core/atomsf.h"
+ 
+ 
+ namespace clipper {
+diff --git a/cctbx_sources/clipper/clipper/contrib/sfcalc_obs.cpp b/cctbx_sources/clipper/clipper/contrib/sfcalc_obs.cpp
+old mode 100755
+new mode 100644
+index de47e09..0f67585
+--- a/cctbx_sources/clipper/clipper/contrib/sfcalc_obs.cpp
++++ b/cctbx_sources/clipper/clipper/contrib/sfcalc_obs.cpp
+@@ -43,8 +43,8 @@
+ 
+ #include "sfcalc_obs.h"
+ #include "edcalc.h"
+-#include "../core/hkl_compute.h"
+-#include "../core/resol_targetfn.h"
++#include "clipper/core/hkl_compute.h"
++#include "clipper/core/resol_targetfn.h"
+ 
+ 
+ namespace clipper {
+diff --git a/cctbx_sources/clipper/clipper/contrib/sfweight.cpp b/cctbx_sources/clipper/clipper/contrib/sfweight.cpp
+old mode 100755
+new mode 100644
+index 1b2d4dc..6ec98c2
+--- a/cctbx_sources/clipper/clipper/contrib/sfweight.cpp
++++ b/cctbx_sources/clipper/clipper/contrib/sfweight.cpp
+@@ -42,8 +42,8 @@
+ 
+ 
+ #include "sfweight.h"
+-#include "../core/hkl_operators.h"
+-#include "../core/resol_targetfn.h"
++#include "clipper/core/hkl_operators.h"
++#include "clipper/core/resol_targetfn.h"
+ 
+ 
+ namespace clipper {
+diff --git a/cctbx_sources/clipper/clipper/contrib/skeleton.cpp b/cctbx_sources/clipper/clipper/contrib/skeleton.cpp
+index bff1049..14ebf55 100644
+--- a/cctbx_sources/clipper/clipper/contrib/skeleton.cpp
++++ b/cctbx_sources/clipper/clipper/contrib/skeleton.cpp
+@@ -42,7 +42,7 @@
+ 
+ #include "skeleton.h"
+ 
+-#include "../core/map_utils.h"
++#include "clipper/core/map_utils.h"
+ 
+ 
+ namespace clipper {
+diff --git a/cctbx_sources/clipper_adaptbx/clipper/SConscript b/cctbx_sources/clipper_adaptbx/clipper/SConscript
+index 1911eb1..df03808 100644
+--- a/cctbx_sources/clipper_adaptbx/clipper/SConscript
++++ b/cctbx_sources/clipper_adaptbx/clipper/SConscript
+@@ -11,5 +11,4 @@ env.SharedLibrary(
+     "clipper_ext.cpp",
+     "hendrickson_lattman_bpl.cpp",
+     "sigmaa_bpl.cpp",
+-    "../../clipper/clipper/contrib/sfweight.cpp",
+     "../../clipper/clipper/cctbx/clipper_cctbx.cpp"]+clipper_contrib_files)

diff --git a/sci-libs/cctbx/files/2012.05.08.2305/0102-dontstrip.patch b/sci-libs/cctbx/files/2012.05.08.2305/0102-dontstrip.patch
new file mode 100644
index 0000000..08118f4
--- /dev/null
+++ b/sci-libs/cctbx/files/2012.05.08.2305/0102-dontstrip.patch
@@ -0,0 +1,25 @@
+ cctbx_sources/libtbx/SConscript | 4 ++--
+ 1 file changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/cctbx_sources/libtbx/SConscript b/cctbx_sources/libtbx/SConscript
+index debf569..46ab8d8 100644
+--- a/cctbx_sources/libtbx/SConscript
++++ b/cctbx_sources/libtbx/SConscript
+@@ -471,7 +471,7 @@ libtbx.scons: Warning: compiling with /MDd:
+     elif libtbx.env.build_options.debug_symbols:
+       lkfl = ["-rdynamic"]
+     else:
+-      lkfl = ["-s"]
++      lkfl = []
+     env_etc.shlinkflags = ["-shared"]
+     if (libtbx.env.build_options.mode == "profile"):
+       env_base.Prepend(LINKFLAGS=["-pg"])
+@@ -589,7 +589,7 @@ else:
+       lkfl = ["-rdynamic"]
+ 
+     else:
+-      lkfl = ["-s"]
++      lkfl = []
+     env_etc.shlinkflags = ["-shared"]
+     if (libtbx.env.build_options.mode == "profile"):
+       env_base.Prepend(LINKFLAGS=["-pg"])

diff --git a/sci-libs/cctbx/files/2013.02.27.0005/0001-remove-hardcoded-libtbx_build-env.patch b/sci-libs/cctbx/files/2013.02.27.0005/0001-remove-hardcoded-libtbx_build-env.patch
new file mode 100644
index 0000000..14d3f09
--- /dev/null
+++ b/sci-libs/cctbx/files/2013.02.27.0005/0001-remove-hardcoded-libtbx_build-env.patch
@@ -0,0 +1,24 @@
+From: =?UTF-8?q?Picca=20Fr=C3=A9d=C3=A9ric-Emmanuel?= <picca@××××××.org>
+Date: Sat, 30 Jun 2012 15:50:22 +0200
+Subject: remove-hardcoded-libtbx_build-env
+
+---
+ cctbx_sources/libtbx/env_config.py |    5 ++++-
+ 1 file changed, 4 insertions(+), 1 deletion(-)
+
+diff --git a/cctbx_sources/libtbx/env_config.py b/cctbx_sources/libtbx/env_config.py
+index 9c01e0f..8a62446 100644
+--- a/cctbx_sources/libtbx/env_config.py
++++ b/cctbx_sources/libtbx/env_config.py
+@@ -2147,7 +2147,10 @@ def cold_start(args):
+   env.refresh()
+ 
+ def unpickle():
+-  build_path = os.environ["LIBTBX_BUILD"]
++  if os.environ.has_key("LIBTBX_BUILD"):
++    build_path = os.environ["LIBTBX_BUILD"]
++  else:
++    build_path = "/usr/share/cctbx/python%d.%d"%(sys.version_info[:2])
+   set_preferred_sys_prefix_and_sys_executable(build_path=build_path)
+   libtbx_env = open(op.join(build_path, "libtbx_env"), "rb")
+   env = pickle.load(libtbx_env)

diff --git a/sci-libs/cctbx/files/2013.02.27.0005/0002-fix-opengl-header-missing-gltbx.patch b/sci-libs/cctbx/files/2013.02.27.0005/0002-fix-opengl-header-missing-gltbx.patch
new file mode 100644
index 0000000..d3684a5
--- /dev/null
+++ b/sci-libs/cctbx/files/2013.02.27.0005/0002-fix-opengl-header-missing-gltbx.patch
@@ -0,0 +1,51 @@
+From: =?UTF-8?q?Picca=20Fr=C3=A9d=C3=A9ric-Emmanuel?= <picca@××××××.org>
+Date: Sat, 30 Jun 2012 15:51:06 +0200
+Subject: fix-opengl-header-missing-gltbx
+
+---
+ cctbx_sources/gltbx/SConscript |   32 ++++++++++++++++----------------
+ 1 file changed, 16 insertions(+), 16 deletions(-)
+
+diff --git a/cctbx_sources/gltbx/SConscript b/cctbx_sources/gltbx/SConscript
+index d02e7a5..4b2213d 100644
+--- a/cctbx_sources/gltbx/SConscript
++++ b/cctbx_sources/gltbx/SConscript
+@@ -45,22 +45,22 @@ if (not env_etc.no_boost_python):
+     env=env,
+     paths=env_etc.gltbx_common_includes + [env_etc.python_include])
+   #
+-  env_etc.gltbx_has_usable_opengl = False
+-  conf = trial_env.Configure()
+-  flag, output = conf.TryRun("""
+-#include <gltbx/include_opengl.h>
+-#include <iostream>
+-int main() { std::cout << GL_POINT << std::endl; return 0; }
+-""", extension=".cpp")
+-  conf.Finish()
+-  if (flag and len(output.strip()) != 0):
+-    conf = env.Configure()
+-    if (conf.TryCompile("""
+-#include <gltbx/include_opengl.h>
+-""", extension=".cpp")):
+-      env_etc.gltbx_has_usable_opengl = True
+-    conf.Finish()
+-  #
++  env_etc.gltbx_has_usable_opengl = True
++#  conf = trial_env.Configure()
++#  flag, output = conf.TryRun("""
++##include <gltbx/include_opengl.h>
++##include <iostream>
++#int main() { std::cout << GL_POINT << std::endl; return 0; }
++#""", extension=".cpp")
++#  conf.Finish()
++#  if (flag and len(output.strip()) != 0):
++#    conf = env.Configure()
++#    if (conf.TryCompile("""
++##include <gltbx/include_opengl.h>
++#""", extension=".cpp")):
++#      env_etc.gltbx_has_usable_opengl = True
++#    conf.Finish()
++#  #
+   if (not env_etc.gltbx_has_usable_opengl):
+     print "gltbx: OpenGL headers and/or libraries not available."
+     print "gltbx: Compilation skipped."

diff --git a/sci-libs/cctbx/files/2013.02.27.0005/0003-correct-paths-in-dispatcher-creation.patch b/sci-libs/cctbx/files/2013.02.27.0005/0003-correct-paths-in-dispatcher-creation.patch
new file mode 100644
index 0000000..8d3a3c2
--- /dev/null
+++ b/sci-libs/cctbx/files/2013.02.27.0005/0003-correct-paths-in-dispatcher-creation.patch
@@ -0,0 +1,86 @@
+From: =?UTF-8?q?Picca=20Fr=C3=A9d=C3=A9ric-Emmanuel?= <picca@××××××.org>
+Date: Sat, 30 Jun 2012 16:01:20 +0200
+Subject: correct-paths-in-dispatcher-creation
+
+---
+ cctbx_sources/libtbx/env_config.py | 48 +++++++++++++++++++-------------------
+ 1 file changed, 24 insertions(+), 24 deletions(-)
+
+diff --git a/cctbx_sources/libtbx/env_config.py b/cctbx_sources/libtbx/env_config.py
+index 8a62446..c3e1c7d 100644
+--- a/cctbx_sources/libtbx/env_config.py
++++ b/cctbx_sources/libtbx/env_config.py
+@@ -932,27 +932,27 @@ Wait for the command to finish, then try again.""" % vars())
+       print >> f, '# command at the end.'
+     print >> f, '#'
+     write_do_not_edit(f=f)
+-    print >> f, '# To customize this auto-generated script create'
++    #print >> f, '# To customize this auto-generated script create'
+     print >> f, '#'
+-    print >> f, '#   dispatcher_include*.sh'
++    #print >> f, '#   dispatcher_include*.sh'
+     print >> f, '#'
+-    print >> f, '# files in %s and run' % show_string(abs(self.build_path))
++    #print >> f, '# files in %s and run' % show_string(abs(self.build_path))
+     print >> f, '#'
+-    print >> f, '#   libtbx.refresh'
++    #print >> f, '#   libtbx.refresh'
+     print >> f, '#'
+     print >> f, '# to re-generate the dispatchers (libtbx.refresh is a subset'
+     print >> f, '# of the functionality of the libtbx/configure.py command).'
+     print >> f, '#'
+-    print >> f, '# See also:'
+-    print >> f, '#   %s' \
+-      % show_string(self.under_build("dispatcher_include_template.sh"))
++    #print >> f, '# See also:'
++    #print >> f, '#   %s' \
++    #  % show_string(self.under_build("dispatcher_include_template.sh"))
+     print >> f, '#'
+     print >> f, _SHELLREALPATH_CODE
+     print >> f, 'unset PYTHONHOME'
+     print >> f, 'LC_ALL=C'
+     print >> f, 'export LC_ALL'
+-    print >> f, 'LIBTBX_BUILD="$(shellrealpath "$0" && cd "$(dirname "$RESULT")/.." && pwd)"'
+-    print >> f, 'export LIBTBX_BUILD'
++    #print >> f, 'LIBTBX_BUILD="$(shellrealpath "$0" && cd "$(dirname "$RESULT")/.." && pwd)"'
++    #print >> f, 'export LIBTBX_BUILD'
+     print >> f, 'LIBTBX_PYEXE_BASENAME="%s"' % self.python_exe.basename()
+     print >> f, 'export LIBTBX_PYEXE_BASENAME'
+     source_is_py = False
+@@ -969,21 +969,21 @@ Wait for the command to finish, then try again.""" % vars())
+         source_is_py = True
+     for line in self.dispatcher_include(where="at_start"):
+       print >> f, line
+-    essentials = [("PYTHONPATH", self.pythonpath)]
+-    essentials.append((
+-      ld_library_path_var_name(),
+-      self.ld_library_path_additions()))
+-    essentials.append(("PATH", [self.bin_path]))
+-    for n,v in essentials:
+-      if (len(v) == 0): continue
+-      v = ":".join([p.sh_value() for p in v])
+-      print >> f, 'if [ -n "$%s" ]; then' % n
+-      print >> f, '  %s="%s:$%s"' % (n, v, n)
+-      print >> f, '  export %s' % n
+-      print >> f, 'else'
+-      print >> f, '  %s="%s"' % (n, v)
+-      print >> f, '  export %s' % n
+-      print >> f, 'fi'
++    # essentials = [("PYTHONPATH", self.pythonpath)]
++    # essentials.append((
++    #   ld_library_path_var_name(),
++    #   self.ld_library_path_additions()))
++    # essentials.append(("PATH", [self.bin_path]))
++    # for n,v in essentials:
++    #   if (len(v) == 0): continue
++    #   v = ":".join([p.sh_value() for p in v])
++    #   print >> f, 'if [ -n "$%s" ]; then' % n
++    #   print >> f, '  %s="%s:$%s"' % (n, v, n)
++    #   print >> f, '  export %s' % n
++    #   print >> f, 'else'
++    #   print >> f, '  %s="%s"' % (n, v)
++    #   print >> f, '  export %s' % n
++    #   print >> f, 'fi'
+     precall_commands = self.dispatcher_precall_commands()
+     if (precall_commands is not None):
+       for line in precall_commands:

diff --git a/sci-libs/cctbx/files/2013.02.27.0005/0006-options-for-system-libs-installtarget-and-prefix.patch b/sci-libs/cctbx/files/2013.02.27.0005/0006-options-for-system-libs-installtarget-and-prefix.patch
new file mode 100644
index 0000000..861d6bc
--- /dev/null
+++ b/sci-libs/cctbx/files/2013.02.27.0005/0006-options-for-system-libs-installtarget-and-prefix.patch
@@ -0,0 +1,1099 @@
+ cctbx_sources/boost_adaptbx/SConscript             |  19 +-
+ cctbx_sources/cbflib_adaptbx/SConscript            |  89 +++---
+ .../detectors/boost_python/SConscript              |   4 +-
+ cctbx_sources/ccp4io_adaptbx/SConscript            | 303 +++++++++++----------
+ cctbx_sources/cctbx/SConscript                     |   2 +-
+ cctbx_sources/clipper_adaptbx/SConscript           |  94 ++++---
+ cctbx_sources/clipper_adaptbx/clipper/SConscript   |  10 +-
+ cctbx_sources/gltbx/SConscript                     |  20 +-
+ cctbx_sources/iotbx/cif/boost_python/SConscript    |  13 +-
+ cctbx_sources/iotbx/mtz/SConscript                 |   3 +-
+ cctbx_sources/iotbx/pdb/SConscript                 |   2 +-
+ cctbx_sources/libtbx/SConscript                    |  84 ++++++
+ cctbx_sources/libtbx/env_config.py                 |  34 +++
+ cctbx_sources/mmtbx/cablam/SConscript              |   2 +-
+ cctbx_sources/mmtbx/den/SConscript                 |   2 +-
+ cctbx_sources/mmtbx/geometry_restraints/SConscript |   2 +-
+ cctbx_sources/mmtbx/secondary_structure/SConscript |   2 +-
+ cctbx_sources/rstbx/SConscript                     |   2 +-
+ cctbx_sources/scitbx/SConscript                    |   2 +-
+ cctbx_sources/scitbx/boost_python/SConscript       |   4 +-
+ .../smtbx/refinement/boost_python/SConscript       |   4 +-
+ .../refinement/constraints/boost_python/SConscript |   4 +-
+ cctbx_sources/spotfinder/SConscript                |   2 +-
+ cctbx_sources/xfel/SConscript                      |   2 +-
+ 24 files changed, 443 insertions(+), 262 deletions(-)
+
+diff --git a/cctbx_sources/boost_adaptbx/SConscript b/cctbx_sources/boost_adaptbx/SConscript
+index e4d5994..7f96c04 100644
+--- a/cctbx_sources/boost_adaptbx/SConscript
++++ b/cctbx_sources/boost_adaptbx/SConscript
+@@ -9,7 +9,13 @@ import sys, os
+ op = os.path
+ Import("env_base", "env_etc")
+ env_etc.boost_dist = libtbx.env.dist_path("boost")
+-env_etc.boost_include = env_etc.boost_dist
++if not env_etc.check_syslib(env_etc.boost_python, extra_libs=env_etc.py_lib)\
++    or not env_etc.check_syslib('boost_thread'):
++  env_etc.boost_include = env_etc.boost_dist
++else:
++  # This way the compiler looks in the standard location for includes
++  # should work on all platforms.
++  env_etc.boost_include = ''
+ env_etc.boost_adaptbx_dist = libtbx.env.dist_path("boost_adaptbx")
+ env_etc.boost_adaptbx_include = os.path.dirname(env_etc.boost_adaptbx_dist)
+ 
+@@ -28,7 +34,7 @@ if (not env_etc.no_boost_python):
+   env_no_includes_boost_python_ext = env_base.Clone(
+     SHLINKFLAGS=env_etc.shlinkflags_bpl,
+     SHLIBPREFIX="",
+-    LIBS=["boost_python"] + env_etc.libs_python + env_etc.libm)
++    LIBS=[env_etc.boost_python] + env_etc.libs_python + env_etc.libm)
+   env_no_includes_boost_python_ext.Append(
+     LIBPATH=env_etc.libpath_python)
+   env_no_includes_boost_python_ext.Append(
+@@ -215,10 +221,11 @@ object/function_doc_signature.cpp
+   bpl_dll_sources = [os.path.join(prefix, path) for path in bpl_dll_sources]
+   #
+   env.Repository(os.path.dirname(env_etc.boost_dist))
+-  if (env_etc.static_bpl):
+-    env.StaticLibrary(target="#lib/boost_python", source=bpl_dll_sources)
+-  else:
+-    env.SharedLibrary(target="#lib/boost_python", source=bpl_dll_sources)
++  if not env_etc.check_syslib(env_etc.boost_python, extra_libs=env_etc.py_lib):
++    if (env_etc.static_bpl):
++      env.StaticLibrary(target="#lib/boost_python", source=bpl_dll_sources)
++    else:
++      env.SharedLibrary(target="#lib/boost_python", source=bpl_dll_sources)
+   if (bool(int(ARGUMENTS.get("boost_python_tests", "0")))):
+     warn_if_unexpected_md5_hexdigest(
+       path=libtbx.env.under_dist("boost", "libs/python/test/Jamfile.v2"),
+diff --git a/cctbx_sources/cbflib_adaptbx/SConscript b/cctbx_sources/cbflib_adaptbx/SConscript
+index 4ac6717..334cfc2 100644
+--- a/cctbx_sources/cbflib_adaptbx/SConscript
++++ b/cctbx_sources/cbflib_adaptbx/SConscript
+@@ -3,9 +3,14 @@ import os
+ Import("env_base","env_etc")
+ 
+ env_etc.cbflib_dist = libtbx.env.dist_path("cbflib")
+-env_etc.cbflib_include = [env_etc.norm_join(env_etc.cbflib_dist,"examples"),
+-                          env_etc.norm_join(env_etc.cbflib_dist,"include"),
+-                          ]
++if not env_etc.check_syslib('cbf'):
++  env_etc.cbflib_include = [env_etc.norm_join(env_etc.cbflib_dist,"examples"),
++                            env_etc.norm_join(env_etc.cbflib_dist,"include"),
++                            ]
++else:
++  env_etc.cbflib_include = [env_etc.norm_join(env_etc.cbflib_dist,"examples"),
++                            "",
++                            ]
+ env_etc.cbflib_adaptbx_dist = libtbx.env.dist_path("cbflib_adaptbx")
+ 
+ env_etc.cbflib_common_includes = [
+@@ -34,39 +39,47 @@ cbflib_092_forward = []
+ if os.path.isfile( os.path.join(env_etc.cbflib_dist,"src","cbf_ws.c") ):
+   cbflib_092_forward.append("src/cbf_ws.c")
+ 
+-env.StaticLibrary(target='#lib/cbf',
+-  source = [prefix+"/"+s for s in [
+-    "examples/img.c",
+-    "src/cbf.c",
+-    "src/cbf_alloc.c",
+-    "src/cbf_ascii.c",
+-    "src/cbf_binary.c",
+-    "src/cbf_byte_offset.c",
+-    "src/cbf_canonical.c",
+-    "src/cbf_codes.c",
+-    "src/cbf_compress.c",
+-    "src/cbf_context.c",
+-    "src/cbf_file.c",
+-    "src/cbf_lex.c",
+-    "src/cbf_packed.c",
+-    "src/cbf_predictor.c",
+-    "src/cbf_read_binary.c",
+-    "src/cbf_read_mime.c",
+-    "src/cbf_simple.c",
+-    "src/cbf_string.c",
+-    "src/cbf_stx.c",
+-    "src/cbf_tree.c",
+-    "src/cbf_uncompressed.c",
+-    "src/cbf_write.c",
+-    "src/cbf_write_binary.c",
+-    "src/md5c.c",
+-  ] + cbflib_092_forward ] + [
+-    "detectors/mar_adaptor.cpp",
+-    "detectors/cbf_adaptor.cpp",
+-    "detectors/cbf_byte_offset_optimized.cpp",
+-    "detectors/buffer_based_service.cpp",
+-  ],
+-  CPPPATH=env_etc.cbflib_common_includes )
++cbflib_src = ["src/cbf.c",
++              "src/cbf_alloc.c",
++              "src/cbf_ascii.c",
++              "src/cbf_binary.c",
++              "src/cbf_byte_offset.c",
++              "src/cbf_canonical.c",
++              "src/cbf_codes.c",
++              "src/cbf_compress.c",
++              "src/cbf_context.c",
++              "src/cbf_file.c",
++              "src/cbf_lex.c",
++              "src/cbf_packed.c",
++              "src/cbf_predictor.c",
++              "src/cbf_read_binary.c",
++              "src/cbf_read_mime.c",
++              "src/cbf_simple.c",
++              "src/cbf_string.c",
++              "src/cbf_stx.c",
++              "src/cbf_tree.c",
++              "src/cbf_uncompressed.c",
++              "src/cbf_write.c",
++              "src/cbf_write_binary.c",
++              "src/md5c.c",
++             ]
++adaptor_src = ["detectors/mar_adaptor.cpp",
++               "detectors/cbf_adaptor.cpp",
++               "detectors/cbf_byte_offset_optimized.cpp",
++               "detectors/buffer_based_service.cpp",
++              ]
++if not env_etc.check_syslib('cbf'):
++  env.StaticLibrary(target='#lib/cbf',
++    source = [prefix+"/"+s for s in [
++      "examples/img.c"] + cbflib_src + cbflib_092_forward] + adaptor_src,
++    CPPPATH=env_etc.cbflib_common_includes )
++  env_etc.cbf_lib = ['cbf',]
++else:
++  env.StaticLibrary(target='#lib/cbf_adaptor',
++    source = [prefix+"/"+s for s in [
++      "examples/img.c"]] + adaptor_src,
++    CPPPATH=env_etc.cbflib_common_includes )
++  env_etc.cbf_lib = ['cbf','cbf_adaptor']
+ 
+ if (not env_etc.no_boost_python):
+   Import("env_no_includes_boost_python_ext")
+@@ -80,7 +93,7 @@ if (not env_etc.no_boost_python):
+   env_cbflib_boost_python_ext.SharedLibrary(
+     target='#lib/_pycbf',
+     source=[prefix+"/pycbf/pycbf_wrap.c"],
+-    LIBS=["cbf"]+env_etc.libs_python+env_etc.libm)
++    LIBS=env_etc.cbf_lib+env_etc.libs_python+env_etc.libm)
+ 
+   Export("env_cbflib_boost_python_ext")
+ 
+@@ -89,7 +102,7 @@ if (not env_etc.no_boost_python):
+ env_standalone = env.Clone(
+   LIBS = [env_etc.libm,],CPPPATH=env_etc.cbflib_common_includes
+ )
+-env_standalone.Prepend(LIBS=["cbf",])
++env_standalone.Prepend(LIBS=env_etc.cbf_lib)
+ 
+ for source in ["detectors/tst_memory",]:
+   target = "cbflib."+os.path.basename(source)
+diff --git a/cctbx_sources/cbflib_adaptbx/detectors/boost_python/SConscript b/cctbx_sources/cbflib_adaptbx/detectors/boost_python/SConscript
+index 2027439..8e987cc 100644
+--- a/cctbx_sources/cbflib_adaptbx/detectors/boost_python/SConscript
++++ b/cctbx_sources/cbflib_adaptbx/detectors/boost_python/SConscript
+@@ -1,6 +1,6 @@
+-Import("env_cbflib_boost_python_ext")
++Import("env_cbflib_boost_python_ext", "env_etc")
+ env = env_cbflib_boost_python_ext.Clone()
+-env.Prepend(LIBS=["cbf",])
++env.Prepend(LIBS=env_etc.cbf_lib)
+ env.SharedLibrary(
+   target="#lib/cbflib_ext",
+   source=["cbflib_ext.cpp",])
+diff --git a/cctbx_sources/ccp4io_adaptbx/SConscript b/cctbx_sources/ccp4io_adaptbx/SConscript
+index 0356403..856115a 100644
+--- a/cctbx_sources/ccp4io_adaptbx/SConscript
++++ b/cctbx_sources/ccp4io_adaptbx/SConscript
+@@ -43,122 +43,167 @@ else:
+   # clean out after completely removing support for
+   # old CCP4 directory structure above
+ 
+-build_ccp4io_adaptbx = libtbx.env.under_build("ccp4io_adaptbx")
+-if (not op.isdir(build_ccp4io_adaptbx)):
+-  os.mkdir(build_ccp4io_adaptbx)
+-  assert op.isdir(build_ccp4io_adaptbx)
+-
+-def replace_printf(file_name):
+-  full_path = op.join(path_lib_src, file_name)
+-  if (not op.isfile(full_path)):
+-    full_path = op.join(op.dirname(path_lib_src), "fortran", file_name)
+-  result = ["#include <ccp4io_adaptbx/printf_wrappers.h>"]
+-  for line in open(full_path).read().splitlines():
+-    for key in ["printf", "fprintf"]:
+-      matches = list(re.finditer(
+-        pattern="[^A-Za-z0-9_]%s[^A-Za-z0-9_]" % key, string=line))
+-      if (len(matches) != 0):
+-        for m in reversed(matches):
+-          s,e = m.start(), m.end()
+-          line = line[:s] \
+-               + line[s:e].replace(key, "ccp4io_%s" % key) \
+-               + line[e:]
+-    result.append(line)
+-  return "\n".join(result)
+-
+-env = env_base.Clone(
+-  SHLINKFLAGS=env_etc.shlinkflags)
+-env.Append(CCFLAGS=env_etc.ccp4io_defines)
+-env.Append(SHCCFLAGS=env_etc.ccp4io_defines)
+-env_etc.include_registry.append(
+-  env=env,
+-  paths=[
+-    "#",
+-    op.dirname(env_etc.ccp4io_include),
+-    env_etc.ccp4io_include,
+-    op.join(env_etc.ccp4io_dist, "lib", mmdb_src),
+-    op.join(env_etc.ccp4io_dist, "lib", mmdb_src, "mmdb")])
+-env.Append(LIBS=env_etc.libm)
+-# XXX 2012-06-16: is this actually necessary here, or just in code that links to
+-# ccp4io.lib?
+-if (os.name == "nt") :
+-  env.Prepend(LIBS=["Advapi32"])
+-if (   op.normcase(op.dirname(env_etc.ccp4io_dist))
+-    != op.normcase("ccp4io")):
+-  env.Repository(op.dirname(env_etc.ccp4io_dist))
+ source = []
+-
+ c_files = []
+-c_files.extend(["%s/%s" % (ccp4_src, bn ) for bn in """\
+-library_err.c
+-library_file.c
+-library_utils.c
+-ccp4_array.c
+-ccp4_parser.c
+-ccp4_unitcell.c
+-cvecmat.c
+-cmtzlib.c
+-""".splitlines()])
+-open(op.join(build_ccp4io_adaptbx, "csymlib.c"), "w").write(
+-  open(op.join(path_lib_src, "csymlib.c")).read()
+-    .replace(
+-      "static int reported_syminfo = 0",
+-      "static int reported_syminfo = 1"))
+-source.append(op.join("#ccp4io_adaptbx", "csymlib.c"))
++if not env_etc.check_syslib('ccp4c')\
++  or not env_etc.check_syslib('mmdb'):
++  build_ccp4io_adaptbx = libtbx.env.under_build("ccp4io_adaptbx")
++  if (not op.isdir(build_ccp4io_adaptbx)):
++    os.mkdir(build_ccp4io_adaptbx)
++    assert op.isdir(build_ccp4io_adaptbx)
++
++  def replace_printf(file_name):
++    full_path = op.join(path_lib_src, file_name)
++    if (not op.isfile(full_path)):
++      full_path = op.join(op.dirname(path_lib_src), "fortran", file_name)
++    result = ["#include <ccp4io_adaptbx/printf_wrappers.h>"]
++    for line in open(full_path).read().splitlines():
++      for key in ["printf", "fprintf"]:
++        matches = list(re.finditer(
++          pattern="[^A-Za-z0-9_]%s[^A-Za-z0-9_]" % key, string=line))
++        if (len(matches) != 0):
++          for m in reversed(matches):
++            s,e = m.start(), m.end()
++            line = line[:s] \
++                 + line[s:e].replace(key, "ccp4io_%s" % key) \
++                 + line[e:]
++      result.append(line)
++    return "\n".join(result)
++  env = env_base.Clone(
++    SHLINKFLAGS=env_etc.shlinkflags)
++  env.Append(CCFLAGS=env_etc.ccp4io_defines)
++  env.Append(SHCCFLAGS=env_etc.ccp4io_defines)
++  env_etc.include_registry.append(
++    env=env,
++    paths=[
++      "#",
++      op.dirname(env_etc.ccp4io_include),
++      env_etc.ccp4io_include,
++      op.join(env_etc.ccp4io_dist, "lib", mmdb_src),
++      op.join(env_etc.ccp4io_dist, "lib", mmdb_src, "mmdb")])
++
++  env.Append(LIBS=env_etc.libm)
++  # XXX 2012-06-16: is this actually necessary here, or just in code that links to
++  # ccp4io.lib?
++  if (os.name == "nt") :
++    env.Prepend(LIBS=["Advapi32"])
++  if (   op.normcase(op.dirname(env_etc.ccp4io_dist))
++      != op.normcase("ccp4io")):
++    env.Repository(op.dirname(env_etc.ccp4io_dist))
+ 
+-probe_file_name = op.join(path_lib_src, "cmaplib.h")
+-env_etc.ccp4io_has_cmaplib = op.isfile(probe_file_name)
+-if (env_etc.ccp4io_has_cmaplib):
+   c_files.extend(["%s/%s" % (ccp4_src, bn ) for bn in """\
+-cmap_accessor.c
+-cmap_close.c
+-cmap_data.c
+-cmap_header.c
+-cmap_labels.c
+-cmap_open.c
+-cmap_skew.c
+-cmap_stats.c
+-cmap_symop.c
+-""".splitlines()])
++  library_err.c
++  library_file.c
++  library_utils.c
++  ccp4_array.c
++  ccp4_parser.c
++  ccp4_unitcell.c
++  cvecmat.c
++  cmtzlib.c
++  """.splitlines()])
++  open(op.join(build_ccp4io_adaptbx, "csymlib.c"), "w").write(
++    open(op.join(path_lib_src, "csymlib.c")).read()
++      .replace(
++        "static int reported_syminfo = 0",
++        "static int reported_syminfo = 1"))
++  source.append(op.join("#ccp4io_adaptbx", "csymlib.c"))
+ 
+-c_files.extend(["%s/mmdb/%s.cpp" % ( mmdb_src, bn ) for bn in """\
+-bfgs_min
+-file_
+-hybrid_36
+-linalg_
+-machine_
+-math_
+-mattype_
+-mmdb_align
+-mmdb_atom
+-mmdb_bondmngr
+-mmdb_chain
+-mmdb_cifdefs
+-mmdb_coormngr
+-mmdb_cryst
+-mmdb_ficif
+-mmdb_file
+-mmdb_graph
+-mmdb_manager
+-mmdb_mask
+-mmdb_mmcif
+-mmdb_model
+-mmdb_rwbrook
+-mmdb_sbase
+-mmdb_sbase0
+-mmdb_selmngr
+-mmdb_symop
+-mmdb_tables
+-mmdb_title
+-mmdb_uddata
+-mmdb_utils
+-mmdb_xml
+-random_n
+-stream_
+-""".splitlines()])
+-prefix = "#"+op.join(op.basename(env_etc.ccp4io_dist), "lib")
+-for file_name in c_files:
+-  source.append(op.join(prefix, file_name))
++  probe_file_name = op.join(path_lib_src, "cmaplib.h")
++  env_etc.ccp4io_has_cmaplib = op.isfile(probe_file_name)
++  if (env_etc.ccp4io_has_cmaplib):
++    c_files.extend(["%s/%s" % (ccp4_src, bn ) for bn in """\
++  cmap_accessor.c
++  cmap_close.c
++  cmap_data.c
++  cmap_header.c
++  cmap_labels.c
++  cmap_open.c
++  cmap_skew.c
++  cmap_stats.c
++  cmap_symop.c
++  """.splitlines()])
++
++  c_files.extend(["%s/mmdb/%s.cpp" % ( mmdb_src, bn ) for bn in """\
++  bfgs_min
++  file_
++  hybrid_36
++  linalg_
++  machine_
++  math_
++  mattype_
++  mmdb_align
++  mmdb_atom
++  mmdb_bondmngr
++  mmdb_chain
++  mmdb_cifdefs
++  mmdb_coormngr
++  mmdb_cryst
++  mmdb_ficif
++  mmdb_file
++  mmdb_graph
++  mmdb_manager
++  mmdb_mask
++  mmdb_mmcif
++  mmdb_model
++  mmdb_rwbrook
++  mmdb_sbase
++  mmdb_sbase0
++  mmdb_selmngr
++  mmdb_symop
++  mmdb_tables
++  mmdb_title
++  mmdb_uddata
++  mmdb_utils
++  mmdb_xml
++  random_n
++  stream_
++  """.splitlines()])
++  prefix = "#"+op.join(op.basename(env_etc.ccp4io_dist), "lib")
++  for file_name in c_files:
++    source.append(op.join(prefix, file_name))
++
++  ssm_prefix = "#"+op.join(op.basename(env_etc.ccp4io_dist), "lib", "ssm")
++  ssm_sources = """\
++  ss_csia.cpp
++  ss_graph.cpp
++  ss_vxedge.cpp
++  ssm_align.cpp
++  ssm_superpose.cpp
++  """.splitlines()
++  source.extend( [ op.join( ssm_prefix, f ) for f in ssm_sources ] )
++
++  need_f_c = (
++       libtbx.env.has_module("solve_resolve")
++    or libtbx.env.find_in_repositories(relative_path="mosflm_fable"))
++  if (need_f_c or os.name != "nt"):
++    source.append(op.join("#ccp4io_adaptbx", "fortran_call_stubs.c"))
++    for file_name in """\
++  ccp4_diskio_f.c
++  ccp4_general.c
++  ccp4_general_f.c
++  ccp4_parser_f.c
++  ccp4_program.c
++  ccp4_unitcell_f.c
++  cmaplib_f.c
++  cmtzlib_f.c
++  csymlib_f.c
++  library_f.c
++  """.splitlines():
++      open(op.join(build_ccp4io_adaptbx, file_name), "w").write(
++        replace_printf(file_name=file_name))
++      source.append(op.join("#ccp4io_adaptbx", file_name))
++    source.append(op.join("#ccp4io_adaptbx", "printf_wrappers.c"))
++  env_etc.ccp4io_lib = "ccp4io"
++  mmdb_path= [ os.path.join( env_etc.ccp4io_dist, "lib", mmdb_src ),
++               os.path.join( env_etc.ccp4io_dist, "lib", mmdb_src, "mmdb" ),
++             ]
++else:
++  env = env_base.Clone(
++    SHLINKFLAGS=env_etc.shlinkflags)
++  env.Append(CCFLAGS=env_etc.ccp4io_defines)
++  env.Append(SHCCFLAGS=env_etc.ccp4io_defines)
++  env_etc.ccp4io_lib = ["ccp4io", "mmdb", "ccp4c"]
++  mmdb_path= []
+ 
+ ssm_prefix = "#"+op.join(op.basename(env_etc.ccp4io_dist), "lib", "ssm")
+ ssm_sources = """\
+@@ -170,46 +215,20 @@ ssm_superpose.cpp
+ """.splitlines()
+ source.extend( [ op.join( ssm_prefix, f ) for f in ssm_sources ] )
+ 
+-need_f_c = (
+-     libtbx.env.has_module("solve_resolve")
+-  or libtbx.env.find_in_repositories(relative_path="mosflm_fable"))
+-if (need_f_c or os.name != "nt"):
+-  source.append(op.join("#ccp4io_adaptbx", "fortran_call_stubs.c"))
+-  for file_name in """\
+-ccp4_diskio_f.c
+-ccp4_general.c
+-ccp4_general_f.c
+-ccp4_parser_f.c
+-ccp4_program.c
+-ccp4_unitcell_f.c
+-cmaplib_f.c
+-cmtzlib_f.c
+-csymlib_f.c
+-library_f.c
+-""".splitlines():
+-    open(op.join(build_ccp4io_adaptbx, file_name), "w").write(
+-      replace_printf(file_name=file_name))
+-    source.append(op.join("#ccp4io_adaptbx", file_name))
+-  source.append(op.join("#ccp4io_adaptbx", "printf_wrappers.c"))
+-
+ # static library for solve_resolve
+ env.StaticLibrary(target='#lib/ccp4io', source=source)
+-env_etc.ccp4io_lib = "ccp4io"
+ 
+ if (    libtbx.env.has_module("boost")
+     and not env_etc.no_boost_python):
+   Import( "env_no_includes_boost_python_ext" )
+   sources = [ "#ccp4io_adaptbx/ext.cpp" ]
+   env_ext = env_no_includes_boost_python_ext.Clone()
+-  env_ext.Prepend( LIBS = "ccp4io" )
++  env_ext.Prepend( LIBS = env_etc.ccp4io_lib )
+   env_etc.include_registry.append(
+     env = env_ext,
+-    paths = [
+-      os.path.join( env_etc.ccp4io_dist, "lib", mmdb_src ),
+-      os.path.join( env_etc.ccp4io_dist, "lib", mmdb_src, "mmdb" ),
+-      os.path.join( env_etc.ccp4io_dist, "lib", "ssm"),
+-      env_etc.boost_include,
+-      env_etc.python_include,
+-      ]
++    paths = mmdb_path + [ os.path.join( env_etc.ccp4io_dist, "lib", "ssm"),
++                          env_etc.boost_include,
++                          env_etc.python_include,
++                        ]
+     )
+   env_ext.SharedLibrary( target = "#lib/ccp4io_adaptbx_ext", source = sources )
+diff --git a/cctbx_sources/cctbx/SConscript b/cctbx_sources/cctbx/SConscript
+index 162f019..1321069 100644
+--- a/cctbx_sources/cctbx/SConscript
++++ b/cctbx_sources/cctbx/SConscript
+@@ -108,7 +108,7 @@ if (not env_etc.no_boost_python):
+   Import("env_no_includes_boost_python_ext")
+ 
+   env_cctbx_boost_python_ext = env_no_includes_boost_python_ext.Clone()
+-  env_cctbx_boost_python_ext.Prepend(LIBS=["scitbx_boost_python"])
++  env_cctbx_boost_python_ext.Prepend(LIBS=[env_etc.scitbx_boost_python])
+   env_etc.include_registry.append(
+     env=env_cctbx_boost_python_ext,
+     paths=env_etc.cctbx_common_includes + [env_etc.python_include])
+diff --git a/cctbx_sources/clipper_adaptbx/SConscript b/cctbx_sources/clipper_adaptbx/SConscript
+index 9cce49e..c39047f 100644
+--- a/cctbx_sources/clipper_adaptbx/SConscript
++++ b/cctbx_sources/clipper_adaptbx/SConscript
+@@ -3,54 +3,63 @@ Import("env_base", "env_etc")
+ 
+ env_etc.clipper_dist = libtbx.env.dist_path("clipper")
+ env_etc.clipper_include = env_etc.clipper_dist
++# This way the compiler looks in the standard location for includes
++# should work on all platforms
++env_etc.clipper_sysinclude = ''
+ 
+ env = env_base.Clone(
+   SHLINKFLAGS=env_etc.shlinkflags,
+   LIBS=env_etc.libm)
+-env.Prepend(CPPPATH=[env_etc.clipper_include])
+-
+-if (env_etc.static_libraries): builder = env.StaticLibrary
+-else:                          builder = env.SharedLibrary
+-builder(target='#lib/clipper',
+-  source = ["../clipper/clipper/core/"+file_name for file_name in """
+-  atomsf.cpp
+-  cell.cpp
+-  clipper_memory.cpp
+-  clipper_message.cpp
+-  clipper_stats.cpp
+-  clipper_types.cpp
+-  clipper_util.cpp
+-  container.cpp
+-  container_hkl.cpp
+-  container_map.cpp
+-  container_types.cpp
+-  coords.cpp
+-  derivs.cpp
+-  hkl_compute.cpp
+-  hkl_data.cpp
+-  hkl_datatypes.cpp
+-  hkl_info.cpp
+-  hkl_lookup.cpp
+-  hkl_operators.cpp
+-  map_interp.cpp
+-  map_utils.cpp
+-  nxmap.cpp
+-  nxmap_operator.cpp
+-  ramachandran.cpp
+-  resol_basisfn.cpp
+-  resol_fn.cpp
+-  resol_targetfn.cpp
+-  rotation.cpp
+-  spacegroup.cpp
+-  spacegroup_data.cpp
+-  symop.cpp
+-  xmap.cpp
+-""".split()])
+-# fftmap_sparse.cpp
+-# fftmap.cpp
++if env_etc.check_syslib('clipper-core') and \
++    env_etc.check_syslib('clipper-contrib'):
++  env.Prepend(CPPPATH=[env_etc.clipper_sysinclude])
++  env_etc.clipper_libs=['clipper-core', 'clipper-contrib']
++  env_etc.has_clipper_contrib = True
++else:
++  env.Prepend(CPPPATH=[env_etc.clipper_include])
++  env_etc.clipper_libs=['clipper',]
++  if (env_etc.static_libraries): builder = env.StaticLibrary
++  else:                          builder = env.SharedLibrary
++  builder(target='#lib/'+env_etc.clipper_libs[0],
++    source = ["../clipper/clipper/core/"+file_name for file_name in """
++    atomsf.cpp
++    cell.cpp
++    clipper_memory.cpp
++    clipper_message.cpp
++    clipper_stats.cpp
++    clipper_types.cpp
++    clipper_util.cpp
++    container.cpp
++    container_hkl.cpp
++    container_map.cpp
++    container_types.cpp
++    coords.cpp
++    derivs.cpp
++    hkl_compute.cpp
++    hkl_data.cpp
++    hkl_datatypes.cpp
++    hkl_info.cpp
++    hkl_lookup.cpp
++    hkl_operators.cpp
++    map_interp.cpp
++    map_utils.cpp
++    nxmap.cpp
++    nxmap_operator.cpp
++    ramachandran.cpp
++    resol_basisfn.cpp
++    resol_fn.cpp
++    resol_targetfn.cpp
++    rotation.cpp
++    spacegroup.cpp
++    spacegroup_data.cpp
++    symop.cpp
++    xmap.cpp
++  """.split()])
++  # fftmap_sparse.cpp
++  # fftmap.cpp
+ 
+ env_exe = env.Clone()
+-env_exe.Prepend(LIBS=["clipper"])
++env_exe.Prepend(LIBS=[env_etc.clipper_libs[0]])
+ 
+ exe = env_exe.Program(
+   target='#exe_dev/'+env["PROGPREFIX"]+'clipper.symtest'
+@@ -77,6 +86,7 @@ if (hasattr(env_etc, "cctbx_include")):
+       env=env_clipper_boost_python_ext,
+       paths=[
+         env_etc.clipper_include,
++        env_etc.clipper_sysinclude,
+         env_etc.libtbx_include,
+         env_etc.cctbx_include,
+         env_etc.scitbx_include,
+diff --git a/cctbx_sources/clipper_adaptbx/clipper/SConscript b/cctbx_sources/clipper_adaptbx/clipper/SConscript
+index 9f79f83..1911eb1 100644
+--- a/cctbx_sources/clipper_adaptbx/clipper/SConscript
++++ b/cctbx_sources/clipper_adaptbx/clipper/SConscript
+@@ -1,6 +1,10 @@
+-Import("env_clipper_boost_python_ext")
++Import("env_clipper_boost_python_ext", "env_etc")
+ env = env_clipper_boost_python_ext.Clone()
+-env.Prepend(LIBS=["clipper", "cctbx"])
++env.Prepend(LIBS=env_etc.clipper_libs+["cctbx"])
++if (env_etc.has_clipper_contrib):
++  clipper_contrib_files = []
++else:
++  clipper_contrib_files = ["../../clipper/clipper/contrib/sfweight.cpp",]
+ env.SharedLibrary(
+   target="#lib/clipper_ext",
+   source=[
+@@ -8,4 +12,4 @@ env.SharedLibrary(
+     "hendrickson_lattman_bpl.cpp",
+     "sigmaa_bpl.cpp",
+     "../../clipper/clipper/contrib/sfweight.cpp",
+-    "../../clipper/clipper/cctbx/clipper_cctbx.cpp"])
++    "../../clipper/clipper/cctbx/clipper_cctbx.cpp"]+clipper_contrib_files)
+diff --git a/cctbx_sources/gltbx/SConscript b/cctbx_sources/gltbx/SConscript
+index d02e7a5..e90f6c3 100644
+--- a/cctbx_sources/gltbx/SConscript
++++ b/cctbx_sources/gltbx/SConscript
+@@ -12,14 +12,15 @@ env_etc.gltbx_common_includes = [
+   env_etc.scitbx_include,
+   env_etc.boost_include,
+ ]
+-if (gl2ps_path is not None):
+-  env_etc.gltbx_common_includes.append(gl2ps_path)
++if not env_etc.check_syslib('gl2ps', extra_libs='GL'):
++  if (gl2ps_path is not None):
++    env_etc.gltbx_common_includes.append(gl2ps_path)
+ 
+ if (not env_etc.no_boost_python):
+   Import("env_base", "env_no_includes_boost_python_ext")
+   trial_env = env_base.Clone()
+   env = env_no_includes_boost_python_ext.Clone()
+-  env.Prepend(LIBS=["scitbx_boost_python"])
++  env.Prepend(LIBS=[env_etc.scitbx_boost_python])
+   if (env_etc.compiler == "win32_cl"):
+     for e in [trial_env, env]:
+       e.Append(LIBS=["glu32", "opengl32"])
+@@ -79,10 +80,15 @@ int main() { std::cout << GL_POINT << std::endl; return 0; }
+         source=source)
+     env_util = env
+     source = ["util_ext.cpp"]
+-    if (gl2ps_path is not None):
+-      source.append("#gui_resources/gl2ps/gl2ps.c")
+-      env_util = env.Clone()
+-      env_util.Append(SHCXXFLAGS=["-DGLTBX_HAVE_GL2PS"])
++    if not env_etc.check_syslib('gl2ps', extra_libs='GL'):
++      if (gl2ps_path is not None):
++        source.append("#gui_resources/gl2ps/gl2ps.c")
++        env_util = env.Clone()
++        env_util.Append(SHCXXFLAGS=["-DGLTBX_HAVE_GL2PS"])
++    else:
++        env_util = env.Clone()
++        env_util.Append(SHCXXFLAGS=["-DGLTBX_HAVE_GL2PS"])
++        env_util.Append(LIBS=["gl2ps"])
+     env_util.SharedLibrary(
+       target="#lib/gltbx_util_ext",
+       source=source)
+diff --git a/cctbx_sources/iotbx/cif/boost_python/SConscript b/cctbx_sources/iotbx/cif/boost_python/SConscript
+index 49837af..2833ff1 100644
+--- a/cctbx_sources/iotbx/cif/boost_python/SConscript
++++ b/cctbx_sources/iotbx/cif/boost_python/SConscript
+@@ -34,15 +34,18 @@ antlr3_src_files = [
+ ]
+ 
+ prefix = "#ucif/antlr3/src"
+-source = [os.path.join(prefix, file_name) for file_name in antlr3_src_files]
++if not env_etc.check_syslib('antlr3c'):
++  source = [os.path.join(prefix, file_name) for file_name in antlr3_src_files]
++  env_etc.include_registry.append(
++    env=env,
++    paths=[antlr3_include, antlr3_dist])
++else:
++  source = []
++  env.Append(LIBS=['antlr3c'])
+ source.extend([
+   "cif_ext.cpp",
+   "#ucif/cifParser.cpp",
+   "#ucif/cifLexer.cpp",
+ ])
+ 
+-env_etc.include_registry.append(
+-  env=env,
+-  paths=[antlr3_include, antlr3_dist])
+-
+ env.SharedLibrary(target="#lib/iotbx_cif_ext", source=source)
+diff --git a/cctbx_sources/iotbx/mtz/SConscript b/cctbx_sources/iotbx/mtz/SConscript
+index 76fb87c..4019731 100644
+--- a/cctbx_sources/iotbx/mtz/SConscript
++++ b/cctbx_sources/iotbx/mtz/SConscript
+@@ -23,7 +23,8 @@ if (not env_etc.no_boost_python):
+   env = env_iotbx_boost_python_ext.Clone()
+   env.Append(CXXFLAGS=env_etc.ccp4io_defines)
+   env.Append(SHCXXFLAGS=env_etc.ccp4io_defines)
+-  env.Prepend(LIBS=["iotbx_mtz", "cctbx", ccp4io_lib, "scitbx_boost_python"])
++  env.Prepend(LIBS=["iotbx_mtz", "cctbx", ccp4io_lib,
++                     env_etc.scitbx_boost_python])
+   if (os.name == "nt") :
+     env.Prepend(LIBS=["Advapi32"])
+   env_etc.enable_more_warnings(env=env)
+diff --git a/cctbx_sources/iotbx/pdb/SConscript b/cctbx_sources/iotbx/pdb/SConscript
+index 6af2664..9b89fe1 100644
+--- a/cctbx_sources/iotbx/pdb/SConscript
++++ b/cctbx_sources/iotbx/pdb/SConscript
+@@ -33,7 +33,7 @@ env.Program(target="hybrid_36_fem", source=["hybrid_36_fem.cpp"])
+ if (not env_etc.no_boost_python):
+   Import("env_iotbx_boost_python_ext")
+   env = env_iotbx_boost_python_ext.Clone()
+-  env.Prepend(LIBS=["iotbx_pdb", "cctbx", "scitbx_boost_python"])
++  env.Prepend(LIBS=["iotbx_pdb", "cctbx", env_etc.scitbx_boost_python])
+   env_etc.enable_more_warnings(env=env)
+   env.SharedLibrary(
+     target="#lib/iotbx_pdb_ext",
+diff --git a/cctbx_sources/libtbx/SConscript b/cctbx_sources/libtbx/SConscript
+index c273536..5aced44 100644
+--- a/cctbx_sources/libtbx/SConscript
++++ b/cctbx_sources/libtbx/SConscript
+@@ -1071,4 +1071,88 @@ def enable_cuda_if_possible():
+ enable_openmp_if_possible()
+ enable_cuda_if_possible()
+ 
++env_etc.use_system_libs = False
++def check_syslib(lib, extra_libs=None):
++  """ Check if a system library is available """
++  if not env_etc.use_system_libs:
++    return False
++  env_syslib = env_base.Clone(LIBS=extra_libs)
++  conf = env_syslib.Configure()
++  if not conf.CheckLib(library=lib):
++    print 'Could not find %s library!'%(lib)
++    conf.Finish()
++    return False
++  else:
++    conf.Finish()
++    return True
++env_etc.check_syslib = check_syslib
++
++env_etc.py_lib = 'python%s.%s'%(sys.version[0], sys.version[2])
++
++if (libtbx.env.build_options.use_system_libs):
++  env_etc.use_system_libs = True
++
++deb_py_str = '-py%s%s'%(sys.version[0], sys.version[2])
++gentoo_py_str = '-%s.%s'%(sys.version[0], sys.version[2])
++# This list can be extended by other distro's
++py_str_lst = [deb_py_str, gentoo_py_str]
++
++for py_str in py_str_lst:
++  if env_etc.check_syslib('boost_python%s'%py_str,
++      extra_libs=env_etc.py_lib):
++    env_etc.boost_python = 'boost_python%s'%py_str
++    env_etc.scitbx_boost_python = 'scitbx_boost_python%s'%py_str
++    break
++  else:
++    env_etc.boost_python = 'boost_python'
++    env_etc.scitbx_boost_python = 'scitbx_boost_python'
++
++env_etc.prefix = libtbx.env.build_options.install_prefix
++env_etc.destdir = libtbx.env.build_options.install_destdir
++env_etc.libdir = libtbx.env.build_options.libdir
++env_etc.install_path = os.path.abspath(env_etc.destdir + '/' + env_etc.prefix)
++env_etc.binpath = os.path.join(env_etc.install_path, 'bin')
++env_etc.libpath = os.path.abspath(env_etc.install_path + '/' + env_etc.libdir)
++env_etc.inclpath = os.path.join(env_etc.install_path, 'include')
++env_etc.rpath = os.path.join(env_etc.prefix, 'lib')
++
++def create_install_targets():
++  cwd = os.getcwd()
++  rp = libtbx.env.repository_paths
++  lib_dir = '%s%s'%(abs(libtbx.env.lib_path), env_etc.rpath)
++  exe_dev = libtbx.env.under_build("exe_dev")
++  include_path = libtbx.env.include_path
++  if not os.path.exists(lib_dir):
++    os.makedirs(lib_dir)
++  rp = list(rp)
++  rp.append(lib_dir)
++  rp.append(include_path)
++  for p in rp:
++    if isinstance(p, str):
++      src_dir = p
++    else:
++      src_dir = abs(p)
++    os.chdir(src_dir)
++    dest = None
++    for root, dirnames, filenames in os.walk('.'):
++      for filename in filenames:
++        if re.match('^lib.*\.(so.*|dylib.*|la|a)$', filename, flags=re.IGNORECASE):
++          dest = os.path.join(env_etc.libpath, root)
++          src = os.path.join(src_dir, root, filename)
++          env_base.Install(dest, src)
++          env_base.Alias("install-shlib", dest)
++        if re.match('^.*\.(h|hpp)$', filename, flags=re.IGNORECASE):
++          dest = os.path.join(env_etc.inclpath, root)
++          src = os.path.join(src_dir, root, filename)
++          env_base.Install(dest, src)
++          env_base.Alias("install-header", dest)
++  dest = env_etc.binpath
++  env_base.Install(dest, Glob('%s/*'%(exe_dev)))
++  env_base.Alias("install-bin", dest)
++  Alias('install', ['install-header', 'install-shlib', 'install-bin'])
++  os.chdir(cwd)
++
++if 'install' in COMMAND_LINE_TARGETS:
++  create_install_targets()
++
+ Export("env_base", "env_etc")
+diff --git a/cctbx_sources/libtbx/env_config.py b/cctbx_sources/libtbx/env_config.py
+index 41b6f91..ddf2848 100644
+--- a/cctbx_sources/libtbx/env_config.py
++++ b/cctbx_sources/libtbx/env_config.py
+@@ -740,6 +740,10 @@ Wait for the command to finish, then try again.""" % vars())
+         precompile_headers=command_line.options.precompile_headers,
+         static_libraries=command_line.options.static_libraries,
+         static_exe=command_line.options.static_exe,
++        use_system_libs=command_line.options.use_system_libs,
++        install_prefix=command_line.options.install_prefix,
++        libdir=command_line.options.libdir,
++        install_destdir=command_line.options.install_destdir,
+         scan_boost=command_line.options.scan_boost,
+         write_full_flex_fwd_h=command_line.options.write_full_flex_fwd_h,
+         boost_python_no_py_signatures
+@@ -1799,6 +1803,10 @@ class build_options:
+         warning_level,
+         static_libraries,
+         static_exe,
++        use_system_libs,
++        install_prefix,
++        libdir,
++        install_destdir,
+         scan_boost,
+         write_full_flex_fwd_h=default_write_full_flex_fwd_h,
+         build_boost_python_extensions=default_build_boost_python_extensions,
+@@ -1860,6 +1868,10 @@ class build_options:
+       self.boost_python_bool_int_strict
+     print >> f, "Enable OpenMP if possible:", self.enable_openmp_if_possible
+     print >> f, "Enable CUDA:", self.enable_cuda
++    print >> f, "Use System Libraries:", self.use_system_libs
++    print >> f, "Install Prefix:", self.install_prefix
++    print >> f, "Libdir:", self.libdir
++    print >> f, "Install Destdir:", self.install_destdir
+     print >> f, "Use opt_resources if available:", self.opt_resources
+     print >> f, "Use environment flags:", self.use_environment_flags
+     if( self.use_environment_flags ):
+@@ -1983,6 +1995,28 @@ class pre_process_args:
+         action="store_true",
+         default=False,
+         help="link all executables statically (implies --static_libraries)")
++      parser.option(None, "--use_system_libs",
++        action="store_true",
++        default=False,
++        help="Use system Libraries to build.")
++      parser.option(None, "--install_destdir",
++        type="string",
++        action="store",
++        default="",
++        help="sets the destdir for the install targets.",
++        metavar="DIRECTORY")
++      parser.option(None, "--libdir",
++        type="string",
++        action="store",
++        default="lib",
++        help="sets the libdir relative to the PREFIX for the install targets. Default: lib",
++        metavar="DIRECTORY")
++      parser.option(None, "--install_prefix",
++        type="string",
++        action="store",
++        default="/usr/local",
++        help="sets the prefix for the install targets. Default: /usr/local",
++        metavar="DIRECTORY")
+       parser.option(None, "--scan_boost",
+         action="store_true",
+         default=False,
+diff --git a/cctbx_sources/mmtbx/cablam/SConscript b/cctbx_sources/mmtbx/cablam/SConscript
+index 67b1edb..36a11bc 100644
+--- a/cctbx_sources/mmtbx/cablam/SConscript
++++ b/cctbx_sources/mmtbx/cablam/SConscript
+@@ -3,7 +3,7 @@ Import("env_etc")
+ if (not env_etc.no_boost_python):
+   Import("env_iotbx_boost_python_ext")
+   env = env_iotbx_boost_python_ext.Clone()
+-  env.Prepend(LIBS=["cctbx", "scitbx_boost_python"])
++  env.Prepend(LIBS=["cctbx", env_etc.scitbx_boost_python])
+   env_etc.enable_more_warnings(env=env)
+   env.SharedLibrary(
+     target="#lib/mmtbx_cablam_align_utils_ext",
+diff --git a/cctbx_sources/mmtbx/den/SConscript b/cctbx_sources/mmtbx/den/SConscript
+index 2d3ce36..1a2b171 100644
+--- a/cctbx_sources/mmtbx/den/SConscript
++++ b/cctbx_sources/mmtbx/den/SConscript
+@@ -3,7 +3,7 @@ Import("env_etc")
+ if (not env_etc.no_boost_python):
+   Import("env_iotbx_boost_python_ext")
+   env = env_iotbx_boost_python_ext.Clone()
+-  env.Prepend(LIBS=["cctbx", "scitbx_boost_python"])
++  env.Prepend(LIBS=["cctbx", env_etc.scitbx_boost_python])
+   env_etc.enable_more_warnings(env=env)
+   env.SharedLibrary(
+     target="#lib/mmtbx_den_restraints_ext",
+diff --git a/cctbx_sources/mmtbx/geometry_restraints/SConscript b/cctbx_sources/mmtbx/geometry_restraints/SConscript
+index b9ee02c..72af551 100644
+--- a/cctbx_sources/mmtbx/geometry_restraints/SConscript
++++ b/cctbx_sources/mmtbx/geometry_restraints/SConscript
+@@ -3,7 +3,7 @@ Import("env_etc")
+ if (not env_etc.no_boost_python):
+   Import("env_iotbx_boost_python_ext")
+   env = env_iotbx_boost_python_ext.Clone()
+-  env.Prepend(LIBS=["cctbx", "scitbx_boost_python"])
++  env.Prepend(LIBS=["cctbx", env_etc.scitbx_boost_python])
+   env_etc.enable_more_warnings(env=env)
+   env.SharedLibrary(
+     target="#lib/mmtbx_hbond_restraints_ext",
+diff --git a/cctbx_sources/mmtbx/secondary_structure/SConscript b/cctbx_sources/mmtbx/secondary_structure/SConscript
+index 7e82b43..5698af5 100644
+--- a/cctbx_sources/mmtbx/secondary_structure/SConscript
++++ b/cctbx_sources/mmtbx/secondary_structure/SConscript
+@@ -3,7 +3,7 @@ Import("env_etc")
+ if (not env_etc.no_boost_python):
+   Import("env_iotbx_boost_python_ext")
+   env = env_iotbx_boost_python_ext.Clone()
+-  env.Prepend(LIBS=["cctbx", "scitbx_boost_python"])
++  env.Prepend(LIBS=["cctbx", env_etc.scitbx_boost_python])
+   env_etc.enable_more_warnings(env=env)
+   env.SharedLibrary(
+     target="#lib/mmtbx_secondary_structure_ext",
+diff --git a/cctbx_sources/rstbx/SConscript b/cctbx_sources/rstbx/SConscript
+index d79b762..a049b88 100644
+--- a/cctbx_sources/rstbx/SConscript
++++ b/cctbx_sources/rstbx/SConscript
+@@ -39,7 +39,7 @@ if (not env_etc.no_boost_python):
+   Import("env_boost_python_ext")
+   env_rstbx_boost_python_ext = env_boost_python_ext.Clone()
+   env_rstbx_boost_python_ext.Prepend(
+-                 LIBS=["rstbx", "cctbx", "scitbx_boost_python"])
++                 LIBS=["rstbx", "cctbx", env_etc.scitbx_boost_python])
+   env_rstbx_boost_python_ext.SharedLibrary(
+                  target="#lib/rstbx_ext", source="ext.cpp")
+   env_rstbx_boost_python_ext.SharedLibrary(
+diff --git a/cctbx_sources/scitbx/SConscript b/cctbx_sources/scitbx/SConscript
+index 9199ae0..6045fbc 100644
+--- a/cctbx_sources/scitbx/SConscript
++++ b/cctbx_sources/scitbx/SConscript
+@@ -28,7 +28,7 @@ SConscript("sparse/tests/SConscript")
+ if (not env_etc.no_boost_python):
+   Import("env_no_includes_boost_python_ext")
+   env_scitbx_boost_python_ext = env_no_includes_boost_python_ext.Clone()
+-  env_scitbx_boost_python_ext.Prepend(LIBS=["scitbx_boost_python"])
++  env_scitbx_boost_python_ext.Prepend(LIBS=[env_etc.scitbx_boost_python])
+   env_etc.include_registry.append(
+     env=env_scitbx_boost_python_ext,
+     paths=env_etc.scitbx_common_includes + [env_etc.python_include])
+diff --git a/cctbx_sources/scitbx/boost_python/SConscript b/cctbx_sources/scitbx/boost_python/SConscript
+index eda7b03..1f396e5 100644
+--- a/cctbx_sources/scitbx/boost_python/SConscript
++++ b/cctbx_sources/scitbx/boost_python/SConscript
+@@ -7,7 +7,7 @@ env_etc.enable_more_warnings(env=env)
+ env.Append(CXXFLAGS=env_etc.cxxflags_bpl_defines_base)
+ env.Append(SHCXXFLAGS=env_etc.cxxflags_bpl_defines_base)
+ env.Append(LIBPATH=env_etc.libpath_python)
+-env.Append(LIBS=["boost_python"] + env_etc.libs_python)
++env.Append(LIBS=[env_etc.boost_python] + env_etc.libs_python)
+ env_etc.include_registry.append(
+   env=env,
+   paths=env_etc.scitbx_common_includes + [env_etc.python_include])
+@@ -20,5 +20,5 @@ lib_scitbx_boost_python_sources = [
+ if (env_etc.static_libraries): builder = env.StaticLibrary
+ else:                          builder = env.SharedLibrary
+ builder(
+-  target="#lib/scitbx_boost_python",
++  target="#lib/%s"%env_etc.scitbx_boost_python,
+   source=lib_scitbx_boost_python_sources)
+diff --git a/cctbx_sources/smtbx/refinement/boost_python/SConscript b/cctbx_sources/smtbx/refinement/boost_python/SConscript
+index 0387e1d..5144996 100644
+--- a/cctbx_sources/smtbx/refinement/boost_python/SConscript
++++ b/cctbx_sources/smtbx/refinement/boost_python/SConscript
+@@ -1,6 +1,6 @@
+-Import("env_smtbx_boost_python_ext")
++Import("env_smtbx_boost_python_ext", "env_etc")
+ env = env_smtbx_boost_python_ext.Clone()
+-env.Prepend(LIBS=["smtbx_refinement_constraints", "scitbx_boost_python"])
++env.Prepend(LIBS=["smtbx_refinement_constraints", env_etc.scitbx_boost_python])
+ env.SharedLibrary(target="#lib/smtbx_refinement_least_squares_ext", source=[
+   "least_squares_ext.cpp",
+   "weighting_schemes.cpp",
+diff --git a/cctbx_sources/smtbx/refinement/constraints/boost_python/SConscript b/cctbx_sources/smtbx/refinement/constraints/boost_python/SConscript
+index 009d288..1eb176b 100644
+--- a/cctbx_sources/smtbx/refinement/constraints/boost_python/SConscript
++++ b/cctbx_sources/smtbx/refinement/constraints/boost_python/SConscript
+@@ -1,5 +1,5 @@
+-Import("env_smtbx_boost_python_ext")
++Import("env_smtbx_boost_python_ext", "env_etc")
+ env = env_smtbx_boost_python_ext.Clone()
+-env.Prepend(LIBS=["smtbx_refinement_constraints", "scitbx_boost_python"])
++env.Prepend(LIBS=["smtbx_refinement_constraints", env_etc.scitbx_boost_python])
+ env.SharedLibrary(target="#lib/smtbx_refinement_constraints_ext",
+                   source=Glob("*.cpp"))
+diff --git a/cctbx_sources/spotfinder/SConscript b/cctbx_sources/spotfinder/SConscript
+index 1d280d4..1d73677 100644
+--- a/cctbx_sources/spotfinder/SConscript
++++ b/cctbx_sources/spotfinder/SConscript
+@@ -54,7 +54,7 @@ if (not env_etc.no_boost_python):
+   Import("env_no_includes_boost_python_ext")
+ 
+   env_spotfinder_boost_python_ext = env_no_includes_boost_python_ext.Clone()
+-  env_spotfinder_boost_python_ext.Prepend(LIBS=[ "scitbx_boost_python"])
++  env_spotfinder_boost_python_ext.Prepend(LIBS=[ env_etc.scitbx_boost_python ])
+   env_etc.include_registry.append(
+     env=env_spotfinder_boost_python_ext,
+     paths=env_etc.spotfinder_common_includes + [env_etc.python_include])
+diff --git a/cctbx_sources/xfel/SConscript b/cctbx_sources/xfel/SConscript
+index e680f73..3397762 100644
+--- a/cctbx_sources/xfel/SConscript
++++ b/cctbx_sources/xfel/SConscript
+@@ -31,7 +31,7 @@ if (not env_etc.no_boost_python):
+   Import("env_boost_python_ext")
+   env_xfel_boost_python_ext = env_boost_python_ext.Clone()
+   env_xfel_boost_python_ext.Prepend(
+-                 LIBS=["cctbx", "scitbx_boost_python"])
++                 LIBS=["cctbx", env_etc.scitbx_boost_python])
+   env_xfel_boost_python_ext.SharedLibrary(
+                  target="#lib/xfel_ext", source="ext.cpp")
+   env_xfel_boost_python_ext.SharedLibrary(

diff --git a/sci-libs/cctbx/files/2013.02.27.0005/0007-adding-shlib-versioning.patch b/sci-libs/cctbx/files/2013.02.27.0005/0007-adding-shlib-versioning.patch
new file mode 100644
index 0000000..fd1888e
--- /dev/null
+++ b/sci-libs/cctbx/files/2013.02.27.0005/0007-adding-shlib-versioning.patch
@@ -0,0 +1,208 @@
+From: Radostan Riedel <raybuntu@××××××××××.com>
+Date: Mon, 23 Jul 2012 18:33:07 +0200
+Subject: adding-shlib-versioning
+
+---
+ cctbx_sources/boost_adaptbx/SConscript |    3 +
+ cctbx_sources/libtbx/SConscript        |  115 +++++++++++++++++++++++++++++---
+ cctbx_sources/libtbx/env_config.py     |    7 ++
+ 3 files changed, 116 insertions(+), 9 deletions(-)
+
+diff --git a/cctbx_sources/boost_adaptbx/SConscript b/cctbx_sources/boost_adaptbx/SConscript
+index 68cac89..dedbb05 100644
+--- a/cctbx_sources/boost_adaptbx/SConscript
++++ b/cctbx_sources/boost_adaptbx/SConscript
+@@ -58,6 +58,9 @@ if (not env_etc.no_boost_python):
+     SHLINKFLAGS=env_etc.shlinkflags_bpl,
+     SHLIBPREFIX="",
+     LIBS=[env_etc.boost_python] + env_etc.libs_python + env_etc.libm)
++  if (libtbx.env.build_options.libtoolize):
++    # Need to unset libtool since it does not support linking python-ext
++    env_etc.unset_libtool(env_no_includes_boost_python_ext)
+   env_no_includes_boost_python_ext.Append(
+     LIBPATH=env_etc.libpath_python)
+   env_no_includes_boost_python_ext.Append(
+diff --git a/cctbx_sources/libtbx/SConscript b/cctbx_sources/libtbx/SConscript
+index 429c44b..58bdd30 100644
+--- a/cctbx_sources/libtbx/SConscript
++++ b/cctbx_sources/libtbx/SConscript
+@@ -1061,16 +1061,99 @@ env_etc.install_path = os.path.abspath(env_etc.destdir + '/' + env_etc.prefix)
+ env_etc.binpath = os.path.join(env_etc.install_path, 'bin')
+ env_etc.libpath = os.path.abspath(env_etc.install_path + '/' + env_etc.libdir)
+ env_etc.inclpath = os.path.join(env_etc.install_path, 'include')
+-env_etc.rpath = os.path.join(env_etc.prefix, 'lib')
++env_etc.rpath = os.path.abspath(env_etc.prefix + '/' + env_etc.libdir)
++
++def set_libtool(env):
++  # Versioning can be provided by appending "-version-info 3:12:1" to SHLINKFLAGS
++  # Please see:
++  # http://www.gnu.org/software/libtool/manual/html_node/Updating-version-info.html
++  # for reference. Otherwise it will be set to 0:0:0
++  env_etc.shobjsuffix_save = env['SHOBJSUFFIX']
++  env_etc.SharedLibBuilder_save = env['BUILDERS']['SharedLibrary']
++  env.Replace(
++    SHLINKFLAGS='-rpath ' + env_etc.rpath,
++    SHOBJSUFFIX='.lo',
++    SHLIBSUFFIX='.la',
++  )
++  LIBTOOLCOM = 'libtool  --mode=compile --tag='
++  LIBTOOLCCOM = LIBTOOLCOM + 'CC '
++  LIBTOOLCXXCOM = LIBTOOLCOM + 'CXX '
++  LIBTOOLLINK = 'libtool  --mode=link --tag=CXX '
++  ShCAction = SCons.Action.Action(LIBTOOLCCOM + "$SHCCCOM", "$SHCCCOMSTR")
++  ShCXXAction = SCons.Action.Action(LIBTOOLCXXCOM + "$SHCXXCOM", "$SHCXXCOMSTR")
++  ShLinkAction = SCons.Action.Action(LIBTOOLLINK + "$SHLINKCOM", "$SHLINKCOMSTR")
++  libtool_install = 'libtool --mode=install install -D ${TARGET.abspath} %s%s/${TARGET.file}'%(abs(libtbx.env.lib_path), env_etc.rpath)
++
++  action_list = [ SCons.Defaults.SharedCheck,
++                  ShLinkAction,
++                  libtool_install,
++                ]
++  CSuffixes = SCons.Tool.cc.CSuffixes
++  # Can't import SCons.Tool.c++.CSuffixes because of that 'c++'
++  CXXSuffixes = ['.cpp', '.cc', '.cxx', '.c++', '.C++', '.mm']
++  shared_obj = SCons.Builder.Builder(action = {},
++                                     emitter = {},
++                                     prefix = '$SHOBJPREFIX',
++                                     suffix = '$SHOBJSUFFIX',
++                                     src_builder = ['CFile', 'CXXFile'],
++                                     source_scanner = SourceFileScanner,
++                                     single_source = 1)
++  for suffix in CXXSuffixes:
++      shared_obj.add_action(suffix, ShCXXAction)
++      shared_obj.add_emitter(suffix, SCons.Defaults.SharedObjectEmitter)
++  for suffix in CSuffixes:
++      shared_obj.add_action(suffix, ShCAction)
++      shared_obj.add_emitter(suffix, SCons.Defaults.SharedObjectEmitter)
++
++  LibtoolBuilder = SCons.Builder.Builder(action = action_list,
++                                     emitter = "$SHLIBEMITTER",
++                                     prefix = '$SHLIBPREFIX',
++                                     suffix = '$SHLIBSUFFIX',
++                                     target_scanner = ProgramScanner,
++                                     src_suffix = '$SHOBJSUFFIX',
++                                     src_builder = shared_obj)
++
++  from SCons.Tool.install import add_targets_to_INSTALLED_FILES
++  LibtoolInstall = SCons.Builder.Builder(
++                        action         = 'libtool --mode=install install -D ${SOURCE.abspath} ${TARGET.abspath}',
++                        target_factory = env.fs.Entry,
++                        source_factory = env.fs.Entry,
++                        multi          = 1,
++                        emitter        = [ add_targets_to_INSTALLED_FILES, ],
++                        name           = 'LibtoolInstall')
++
++  env['BUILDERS']['LibtoolInstall'] = LibtoolInstall
++
++  lib_dir = '%s%s'%(abs(libtbx.env.lib_path), env_etc.rpath)
++  if not os.path.exists(lib_dir):
++    os.makedirs(lib_dir)
++  libtool_install_path = '#lib' + env_etc.rpath
++  env.Append(LIBPATH=libtool_install_path)
++  env['BUILDERS']['SharedLibrary'] = LibtoolBuilder
++env_etc.set_libtool = set_libtool
++
++def unset_libtool(env):
++  env['BUILDERS']['SharedLibrary'] = env_etc.SharedLibBuilder_save
++  env.Replace(
++  SHOBJSUFFIX=env_etc.shobjsuffix_save,
++  )
++env_etc.unset_libtool = unset_libtool
++
++if (libtbx.env.build_options.libtoolize):
++  env_etc.shlibsuffix = ".la"
++  env_base.Append(LIBSUFFIXES=[env_etc.shlibsuffix])
++  rpath_link = ['-rpath', env_etc.rpath]
++  env_etc.shlinkflags.extend(rpath_link)
++  if '-shared' in env_etc.shlinkflags:
++    env_etc.shlinkflags.remove('-shared')
++  env_etc.set_libtool(env_base)
+ 
+ def create_install_targets():
+   cwd = os.getcwd()
+   rp = libtbx.env.repository_paths
+-  lib_dir = '%s%s'%(abs(libtbx.env.lib_path), env_etc.rpath)
++  lib_dir = abs(libtbx.env.lib_path)
+   exe_dev = libtbx.env.under_build("exe_dev")
+   include_path = libtbx.env.include_path
+-  if not os.path.exists(lib_dir):
+-    os.makedirs(lib_dir)
+   rp = list(rp)
+   rp.append(lib_dir)
+   rp.append(include_path)
+@@ -1082,17 +1165,31 @@ def create_install_targets():
+     os.chdir(src_dir)
+     dest = None
+     for root, dirnames, filenames in os.walk('.'):
++      # exclude .libs dir
++      if '.libs' in dirnames:
++        dirnames.remove('.libs')
+       for filename in filenames:
+-        if re.match('^lib.*\.(so.*|dylib.*|la|a)$', filename, flags=re.IGNORECASE):
+-          dest = os.path.join(env_etc.libpath, root)
+-          src = os.path.join(src_dir, root, filename)
+-          env_base.Install(dest, src)
+-          env_base.Alias("install-shlib", dest)
++        if not (libtbx.env.build_options.libtoolize):
++          if re.match('^lib.*\.(so|dylib|a)$', filename, flags=re.IGNORECASE):
++            dest = os.path.join(env_etc.libpath, root)
++            src = os.path.join(src_dir, root, filename)
++            env_base.Install(dest, src)
++            env_base.Alias("install-shlib", dest)
++        else:
++          if re.match('^lib.*\.la$', filename, flags=re.IGNORECASE):
++            dest = os.path.join(env_etc.libpath, root, filename)
++            src = os.path.join(src_dir, root, filename)
++            env_base.LibtoolInstall(dest, src)
++            env_base.Alias("install-shlib", dest)
+         if re.match('^.*\.(h|hpp)$', filename, flags=re.IGNORECASE):
+           dest = os.path.join(env_etc.inclpath, root)
+           src = os.path.join(src_dir, root, filename)
+           env_base.Install(dest, src)
+           env_base.Alias("install-header", dest)
++      if src_dir == lib_dir:
++        break
++
++  env_base.Alias("install-shlib", dest)
+   dest = env_etc.binpath
+   env_base.Install(dest, Glob('%s/*'%(exe_dev)))
+   env_base.Alias("install-bin", dest)
+diff --git a/cctbx_sources/libtbx/env_config.py b/cctbx_sources/libtbx/env_config.py
+index 0885527..3d9133e 100644
+--- a/cctbx_sources/libtbx/env_config.py
++++ b/cctbx_sources/libtbx/env_config.py
+@@ -705,6 +705,7 @@ Wait for the command to finish, then try again.""" % vars())
+         install_prefix=command_line.options.install_prefix,
+         libdir=command_line.options.libdir,
+         install_destdir=command_line.options.install_destdir,
++        libtoolize=command_line.options.libtoolize,
+         scan_boost=command_line.options.scan_boost,
+         write_full_flex_fwd_h=command_line.options.write_full_flex_fwd_h,
+         boost_python_no_py_signatures
+@@ -1767,6 +1768,7 @@ class build_options:
+         install_prefix,
+         libdir,
+         install_destdir,
++        libtoolize,
+         scan_boost,
+         write_full_flex_fwd_h=default_write_full_flex_fwd_h,
+         build_boost_python_extensions=default_build_boost_python_extensions,
+@@ -1830,6 +1832,7 @@ class build_options:
+     print >> f, "Boost threads enabled:", self.enable_boost_threads
+     print >> f, "Enable OpenMP if possible:", self.enable_openmp_if_possible
+     print >> f, "Enable CUDA:", self.enable_cuda
++    print >> f, "Libtoolize:", self.libtoolize
+     print >> f, "Use System Libraries:", self.use_system_libs
+     print >> f, "Install Prefix:", self.install_prefix
+     print >> f, "Libdir:", self.libdir
+@@ -1974,6 +1977,10 @@ class pre_process_args:
+         default="/usr/local",
+         help="sets the prefix for the install targets. Default: /usr/local",
+         metavar="DIRECTORY")
++      parser.option(None, "--libtoolize",
++        action="store_true",
++        default=False,
++        help="build all shared libraries with libtool.")
+       parser.option(None, "--scan_boost",
+         action="store_true",
+         default=False,

diff --git a/sci-libs/cctbx/files/2013.02.27.0005/0008-Fix-to-skip-pycbf-build.patch b/sci-libs/cctbx/files/2013.02.27.0005/0008-Fix-to-skip-pycbf-build.patch
new file mode 100644
index 0000000..7aa3a39
--- /dev/null
+++ b/sci-libs/cctbx/files/2013.02.27.0005/0008-Fix-to-skip-pycbf-build.patch
@@ -0,0 +1,52 @@
+From: Radostan Riedel <raybuntu@××××××××××.com>
+Date: Tue, 7 Aug 2012 18:08:30 +0200
+Subject: Fix to skip pycbf build
+
+---
+ cctbx_sources/cbflib_adaptbx/SConscript        |    8 ++++----
+ cctbx_sources/cbflib_adaptbx/libtbx_refresh.py |   16 ++++++++--------
+ 2 files changed, 12 insertions(+), 12 deletions(-)
+
+diff --git a/cctbx_sources/cbflib_adaptbx/SConscript b/cctbx_sources/cbflib_adaptbx/SConscript
+index 334cfc2..42ab9c3 100644
+--- a/cctbx_sources/cbflib_adaptbx/SConscript
++++ b/cctbx_sources/cbflib_adaptbx/SConscript
+@@ -90,10 +90,10 @@ if (not env_etc.no_boost_python):
+     env=env_cbflib_boost_python_ext,
+     paths=env_etc.cbflib_common_includes + [env_etc.python_include])
+ 
+-  env_cbflib_boost_python_ext.SharedLibrary(
+-    target='#lib/_pycbf',
+-    source=[prefix+"/pycbf/pycbf_wrap.c"],
+-    LIBS=env_etc.cbf_lib+env_etc.libs_python+env_etc.libm)
++  #env_cbflib_boost_python_ext.SharedLibrary(
++  #  target='#lib/_pycbf',
++  #  source=[prefix+"/pycbf/pycbf_wrap.c"],
++  #  LIBS=env_etc.cbf_lib+env_etc.libs_python+env_etc.libm)
+ 
+   Export("env_cbflib_boost_python_ext")
+ 
+diff --git a/cctbx_sources/cbflib_adaptbx/libtbx_refresh.py b/cctbx_sources/cbflib_adaptbx/libtbx_refresh.py
+index 51b3e42..dd1b8e9 100644
+--- a/cctbx_sources/cbflib_adaptbx/libtbx_refresh.py
++++ b/cctbx_sources/cbflib_adaptbx/libtbx_refresh.py
+@@ -1,11 +1,11 @@
+ from libtbx.str_utils import show_string
+ import os
+ op = os.path
+-pycbf_py = self.env.under_dist(module_name="cbflib", path="pycbf/pycbf.py")
+-if (not op.isfile(pycbf_py)):
+-  raise RuntimeError("Missing file: %s" % show_string(pycbf_py))
+-target_dir = self.env.under_build(path="lib")
+-if (not op.isdir(target_dir)):
+-  os.makedirs(target_dir)
+-print "  Copying to lib: %s" % show_string(pycbf_py)
+-open(op.join(target_dir, "pycbf.py"), "w").write(open(pycbf_py).read())
++#pycbf_py = self.env.under_dist(module_name="cbflib", path="pycbf/pycbf.py")
++#if (not op.isfile(pycbf_py)):
++#  raise RuntimeError("Missing file: %s" % show_string(pycbf_py))
++#target_dir = self.env.under_build(path="lib")
++#if (not op.isdir(target_dir)):
++#  os.makedirs(target_dir)
++#print "  Copying to lib: %s" % show_string(pycbf_py)
++#open(op.join(target_dir, "pycbf.py"), "w").write(open(pycbf_py).read())

diff --git a/sci-libs/cctbx/files/2013.02.27.0005/0009-build-libann-statically.patch b/sci-libs/cctbx/files/2013.02.27.0005/0009-build-libann-statically.patch
new file mode 100644
index 0000000..77ba2b2
--- /dev/null
+++ b/sci-libs/cctbx/files/2013.02.27.0005/0009-build-libann-statically.patch
@@ -0,0 +1,27 @@
+From: Radostan Riedel <raybuntu@××××××××××.com>
+Date: Thu, 19 Jul 2012 11:29:57 +0200
+Subject: build libann statically
+
+---
+ cctbx_sources/annlib_adaptbx/SConscript |    8 +++++---
+ 1 file changed, 5 insertions(+), 3 deletions(-)
+
+diff --git a/cctbx_sources/annlib_adaptbx/SConscript b/cctbx_sources/annlib_adaptbx/SConscript
+index 31b4da6..f217b3f 100644
+--- a/cctbx_sources/annlib_adaptbx/SConscript
++++ b/cctbx_sources/annlib_adaptbx/SConscript
+@@ -29,9 +29,11 @@ if (libtbx.manual_date_stamp < 20090819):
+   env.Replace(CXXFLAGS=env_etc.cxxflags_base)
+   env.Replace(SHCXXFLAGS=env_etc.cxxflags_base)
+ 
+-if (env_etc.static_libraries): builder = env.StaticLibrary
+-else:                          builder = env.SharedLibrary
+-builder(target='#lib/ann',
++#if (env_etc.static_libraries): builder = env.StaticLibrary
++#else:                          builder = env.SharedLibrary
++# Create a static library since the changes are incompatiple
++# with debian's libann
++env.StaticLibrary(target='#lib/ann',
+   source = ["../annlib/src/ANN.cpp",
+             "../annlib/src/bd_fix_rad_search.cpp",
+             "../annlib/src/bd_pr_search.cpp",

diff --git a/sci-libs/cctbx/files/2013.02.27.0005/0010-adding-setup_py.patch b/sci-libs/cctbx/files/2013.02.27.0005/0010-adding-setup_py.patch
new file mode 100644
index 0000000..7599d82
--- /dev/null
+++ b/sci-libs/cctbx/files/2013.02.27.0005/0010-adding-setup_py.patch
@@ -0,0 +1,662 @@
+From: Baptiste Carvello <devel@×××××××××××××××××.net>
+Date: Tue, 21 Aug 2012 16:10:19 +0200
+Subject: adding-setup_py
+
+---
+ cctbx_sources/stdlib.py |    4 +
+ sconsutils.py           |  485 +++++++++++++++++++++++++++++++++++++++++++++++
+ setup.py                |  136 +++++++++++++
+ 3 files changed, 625 insertions(+)
+ create mode 100755 cctbx_sources/stdlib.py
+ create mode 100644 sconsutils.py
+ create mode 100755 setup.py
+
+diff --git a/cctbx_sources/stdlib.py b/cctbx_sources/stdlib.py
+new file mode 100755
+index 0000000..759f689
+--- /dev/null
++++ b/cctbx_sources/stdlib.py
+@@ -0,0 +1,4 @@
++from libtbx.forward_compatibility import stdlib_import
++
++math = stdlib_import("math")
++random = stdlib_import("random")
+diff --git a/sconsutils.py b/sconsutils.py
+new file mode 100644
+index 0000000..322585b
+--- /dev/null
++++ b/sconsutils.py
+@@ -0,0 +1,485 @@
++from distutils.sysconfig import get_python_lib, get_config_var
++from distutils.command.build_ext import build_ext as _build_ext
++from distutils.command.build_py import build_py as _build_py
++from distutils.command.install_lib import install_lib as _install_lib
++from distutils.command.install_data import install_data as _install_data
++from distutils.command.clean import clean as _clean
++from distutils.cmd import Command as _Command
++from distutils.dir_util import remove_tree
++from distutils.util import change_root, convert_path
++from distutils.errors import DistutilsExecError
++from distutils import log
++import sys, os
++import SCons.Script
++import libtbx
++import libtbx.env_config
++from libtbx.path import relocatable_path, absolute_path
++from libtbx.path import relpath    # don't use relpath from os.path, introduced in 2.6
++from libtbx.utils import import_python_object
++import threading
++import pickle
++
++opj = os.path.join
++configure_list = []
++scons_buildargv = []
++scons_installargv = []
++SRCDIR=''
++
++class Command(_Command):
++    def run_scons(self, argv):
++        cwd = os.getcwd()
++        builddir = opj(os.path.abspath(self.build_temp), 'cctbx-build')    # build_temp must be set by subclass
++        if not os.path.exists(builddir):
++            if not os.path.exists(os.path.abspath(self.build_temp)):
++                os.mkdir(os.path.abspath(self.build_temp))
++            os.mkdir(builddir)
++        elif not os.path.isdir(builddir):
++            raise RuntimeError(("Build directory '%s' cannot be created "
++                                "because of existing file") % builddir)
++        os.chdir(builddir)
++        if '%PREFIX%' in configure_list:
++            idx=configure_list.index('%PREFIX%')
++            configure_list[idx] = self.prefix    # prefix must be set by subclass
++        libtbx.env_config.cold_start(configure_list)
++        os.environ["LIBTBX_BUILD"] = builddir
++        os.environ['PYTHONPATH'] = ':'.join(sys.path)
++        self.spawn(argv)
++        os.chdir(cwd)
++
++class build_ext(_build_ext, Command):
++    user_options = _build_ext.user_options + [
++        ('prefix=', None, "installation prefix (default: python installation prefix")
++    ]
++    def initialize_options(self):
++        _build_ext.initialize_options(self)
++        self.prefix = None
++    def finalize_options(self):
++        _build_ext.finalize_options(self)
++        if not self.prefix:
++            self.prefix = get_config_var('prefix')    # on Debian: 'usr'
++    def run(self):
++        builddir = opj(os.path.abspath(self.build_temp), 'cctbx-build')    # build_temp set by _build_ext
++        self.run_scons(scons_buildargv)
++        for ext in self.extensions:
++            if len(ext.sources) != 1 or  ext.sources[0] != '%SCONSLIB%':
++                log.warn("Don't know how to build extension '%s' -- skipping",
++                    ext.name)
++                continue
++            dst = self.get_ext_fullpath(ext.name)
++            bld = opj(builddir, 'lib', os.path.basename(dst))
++            if os.path.isfile(bld):
++                self.copy_file(bld, dst)
++
++class build_py(_build_py):
++    def build_module (self, module, module_file, package):
++        if type(package) is str:
++            package = package.split('.')
++        elif type(package) not in (list, tuple):
++            raise TypeError, \
++                  "'package' must be a string (dot-separated), list, or tuple"
++
++        # Now put the module source file into the "build" area -- this is
++        # easy, we just copy it somewhere under self.build_lib (the build
++        # directory for Python source).
++        outfile = self.get_module_outfile(self.build_lib, package, module)
++        dir = os.path.dirname(outfile)
++        self.mkpath(dir)
++        # If the module contains non-blank, non-comment/docstring lines, and doesn't have
++        # the __future__ import, add it before the first non-comment/docstring line
++        empty = True
++        found = False
++        docstring = None
++        file_obj = open(module_file)
++        for line in file_obj:
++            if docstring:
++                if (line.count(docstring) % 2) == 1:
++                    # FIXME this logic will fail with lines such as """ + ''',
++                    # but nobody with a sane mind would do that, would they ?
++                    docstring = None
++                continue
++            if line == "from __future__ import division\n":
++                found = True
++                break
++            if line.isspace() or line.startswith('#'):
++                continue
++            if line.startswith('"""') and (line.count('"""') % 2) == 1:
++                docstring = '"""'
++                continue
++            if line.startswith('"'):
++                continue
++            if line.startswith("'''") and (line.count("'''") % 2) == 1:
++                docstring = "'''"
++                continue
++            if line.startswith("'"):
++                continue
++            empty = False
++            break
++        file_obj.close()
++        if empty or found:
++            return self.copy_file(module_file, outfile, preserve_mode=0)
++        elif self.dry_run:
++            if os.path.isdir(outfile):
++                outfile = opj(outfile, os.path.basename(module_file))
++            log.info("copying with modification %s -> %s", module_file, outfile)
++            return outfile, True
++        else:
++            if os.path.isdir(outfile):
++                outfile = opj(outfile, os.path.basename(module_file))
++            log.info("copying with modification %s -> %s", module_file, outfile)
++            file_obj = open(module_file)
++            outfile_obj = open(outfile, 'w')
++            written = False
++            docstring = None
++            for line in file_obj:
++                if not written:
++                    if docstring:
++                        if (line.count(docstring) % 2) == 1:
++                            docstring = None
++                        outfile_obj.write(line)
++                        continue
++                    if line.isspace() or line.startswith('#'):
++                        outfile_obj.write(line)
++                        continue
++                    if line.startswith('"""') and (line.count('"""') % 2) == 1:
++                        docstring = '"""'
++                        outfile_obj.write(line)
++                        continue
++                    if line.startswith('"'):
++                        outfile_obj.write(line)
++                        continue
++                    if line.startswith("'''") and (line.count("'''") % 2) == 1:
++                        docstring = "'''"
++                        outfile_obj.write(line)
++                        continue
++                    if line.startswith("'"):
++                        outfile_obj.write(line)
++                        continue
++                    outfile_obj.write("from __future__ import division\n")
++                    written = True
++                outfile_obj.write(line)
++            outfile_obj.close()
++            file_obj.close()
++            return outfile, True
++
++class test(_Command):
++    description = "runs the tests in the distutils build directory"
++    user_options = [
++        ('build-lib=', None,
++         "distutils build directory (default: 'build.build-lib')"),
++        ('build-temp=', 't',
++         "directory for temporary files (default: 'build.build-temp')")
++    ]
++    def initialize_options(self):
++        self.build_lib = None
++        self.build_temp = None
++    def finalize_options(self):
++        self.set_undefined_options('build',
++                                   ('build_lib', 'build_lib'),
++                                   ('build_temp', 'build_temp'))
++    def run(self):
++        libdir = os.path.abspath(os.path.abspath(self.build_lib))
++        builddir = opj(os.path.abspath(self.build_temp), 'cctbx-build')
++        testdir = opj(os.path.abspath(self.build_temp), 'cctbx-test')
++        self.setup_test_env(builddir, libdir, testdir)
++        os.environ["LIBTBX_BUILD"] = testdir
++        env = libtbx.env_config.unpickle()
++        os.environ['PYTHONPATH'] = ':'.join([libdir] + sys.path[5:])
++        llp = os.environ.get('LD_LIBRARY_PATH')
++        if llp is not None:
++            os.environ['LD_LIBRARY_PATH'] = ':'.join([opj(builddir, 'lib', '.libs'), llp])
++        else:
++            os.environ['LD_LIBRARY_PATH'] = opj(builddir, 'lib', '.libs')
++        os.chdir(testdir)
++        failed = []
++        for m in env.module_list:
++            for (module_name,dist_path) in m.name_and_dist_path_pairs():
++                try:
++#                    tst_list = import_python_object(
++#                            import_path="%s.run_tests.tst_list" % module_name,    Does not work yet
++#                            error_prefix="",
++#                            target_must_be="",
++#                            where_str="").object 
++                    run_func = import_python_object(
++                            import_path="%s.run_tests.run" % module_name,
++                            error_prefix="",
++                            target_must_be="",
++                            where_str="").object
++                    tst_mod = file(opj(abs(dist_path), "run_tests.py"))    # Ugly, temporary
++                    tst_lines = [l.strip() for l in tst_mod]
++                    tst_mod.close()
++                    tst_code = " ".join(["("] +
++                                        tst_lines[(tst_lines.index("tst_list = (")+1)
++                                                 :(tst_lines.index(")")+1)]
++                                        )
++                    tst_list = eval(tst_code)
++
++                except Exception:
++                    continue
++                for tst in tst_list:    # adapted from libtbx.test_utils.iter_tests_cmd
++                    cmd_args = []
++                    if (type(tst) == type([])):
++#                        cmd_args = tst[1:]    FIXME why only in quick mode?
++                        tst = tst[0]
++                    if (tst.startswith("$B")):
++                        tst_path = tst.replace("$B", builddir)
++                    else:
++                        tst_path = tst.replace("$D", abs(dist_path))
++                    if "$" in tst_path or '"' in tst_path:
++                        log.warn("Could not run test '%s':\n%s", tst, "Unexpected '$' in test path")
++                        failed.append([module_name,tst,AssertionError("Unexpected '$' in test path")])
++                        continue
++                    if '"' in tst_path:
++                        log.warn("Could not run test '%s':\n%s", tst, "Unexpected '\"' in test path")
++                        failed.append([module_name,tst,AssertionError("Unexpected '\"' in test path")])
++                        continue
++                    tst_path = os.path.normpath(tst_path)
++                    if (tst_path.endswith(".py")):
++                        cmd = [sys.executable, tst_path] + cmd_args
++                    else:
++                        cmd = [tst_path] + cmd_args
++                    try:
++                        self.spawn(cmd)
++                    except DistutilsExecError, e:
++                        log.warn("Failure in test '%s':\n%s", tst, str(e))
++                        failed.append([module_name,tst,e])
++                    except Exception, e:
++                        log.warn("Exception in test '%s':\n%s", tst, str(e))
++                        failed.append([module_name,tst,e])
++        if failed:
++            log.warn("Some tests failed:")
++            for n,t,e in failed:
++                log.warn("    module %s, test %s" % (n,t))
++            raise RuntimeError("Test failures")
++
++    def setup_test_env(self, builddir, libdir, testdir):
++        """ Create the test directory and the temporary libtbx_env pickle object """
++        if not os.path.exists(testdir):
++            if not os.path.exists(os.path.abspath(self.build_temp)):
++                os.mkdir(os.path.abspath(self.build_temp))
++            os.mkdir(testdir)
++        elif not os.path.isdir(testdir):
++            raise RuntimeError(("Test directory '%s' cannot be created "
++                                "because of existing file") % testdir)
++        os.environ["LIBTBX_BUILD"] = builddir
++        env = libtbx.env_config.unpickle()
++        module_dist_paths = {}
++        for key, value in env.module_dist_paths.items():
++            head, module = os.path.split(abs(value))
++            module_dist_paths[key] = relocatable_path(absolute_path(libdir), module)
++        env.module_dist_paths = module_dist_paths
++        for module in env.module_list:
++            paths = []
++            for path in module.dist_paths:
++                if path != None:
++                    head, tail = os.path.split(abs(path))
++                    rp = relocatable_path(absolute_path(libdir), tail)
++                    paths.append(rp)
++                else:
++                    paths.append(None)
++            module.dist_paths = paths
++        file_obj = open(opj(testdir,'libtbx_env'), 'wb')
++        pickle.dump(env, file_obj, 0)
++        file_obj.close()
++
++class install_lib(_install_lib, Command):
++    user_options = _install_lib.user_options + [
++        ('build-temp=', 't',
++         "directory for temporary files (default: 'build.build-temp')"),
++        ('prefix=', None, "installation prefix (default: 'install.prefix')"),
++        ('root=', None,
++         "install everything relative to this alternate root directory (default: 'install.root')")
++    ]
++    def initialize_options(self):
++        _install_lib.initialize_options(self)
++        self.build_temp = None
++        self.prefix = None
++        self.root = None
++    def finalize_options(self):
++        _install_lib.finalize_options(self)
++        self.set_undefined_options('build',
++                                   ('build_temp', 'build_temp'))
++        self.set_undefined_options('install',
++                                   ('prefix', 'prefix'),
++                                   ('root', 'root'))
++    def run(self):
++        _install_lib.run(self)
++        if self.root != None:
++            ip = '--install_destdir'
++            if ip not in configure_list:
++                configure_list.extend([ip, self.root])
++        self.run_scons(scons_installargv)
++
++class install_data(_install_data, Command):
++    user_options = _install_data.user_options + [
++        ('build-temp=', 't',
++         "directory for temporary files (default: 'build.build-temp')"),
++        ('prefix=', None, "installation prefix (default: 'install.prefix')")
++    ]
++    def initialize_options(self):
++        _install_data.initialize_options(self)
++        self.build_temp = None
++        self.prefix = None
++    def finalize_options(self):
++        _install_data.finalize_options(self)
++        self.set_undefined_options('build',
++                                   ('build_temp', 'build_temp'))
++        self.set_undefined_options('install',
++                                   ('prefix', 'prefix'))
++    def run(self):
++        # filter the list
++        newdf = []
++        libtbx_env_path = None
++        for f in self.data_files:
++            if type(f) is str:
++                newdf.append(f)
++                continue
++            if '%LIBTBXENV%' in f[1]:
++                f = (f[0], [p for p in f[1] if p != '%LIBTBXENV%'])
++                libtbx_env_path = opj(convert_path(f[0]), 'libtbx_env')
++                if not os.path.isabs(libtbx_env_path):    # mimic the logic in install_data
++                    libtbx_env_path = opj(self.install_dir, libtbx_env_path)
++                elif self.root:
++                    libtbx_env_path = change_root(self.root, libtbx_env_path)
++                # we leave the directory in, so that distutils will create it
++            newdf.append(f)
++        self.data_files = newdf
++        _install_data.run(self)
++        if libtbx_env_path is not None:
++            self.install_libtbx_env(libtbx_env_path)
++            self.outfiles.append(libtbx_env_path)
++
++    def install_libtbx_env(self, libtbx_env_path):
++        """ Modify libtbx_env pickle object to set the correct paths. """
++        builddir = opj(os.path.abspath(self.build_temp), 'cctbx-build')
++        os.environ["LIBTBX_BUILD"] = builddir
++        env = libtbx.env_config.unpickle()
++        env.build_path = absolute_path(self.prefix)
++        build_path = env.build_path
++        python_lib = get_python_lib()
++        rel_path = opj(python_lib, 'cctbx')
++        env.bin_path = relocatable_path(build_path, 'bin')
++        env.lib_path = relocatable_path(build_path, 'lib')
++        env.include_path = relocatable_path(build_path, 'include')
++        env.repository_paths = relocatable_path(build_path, rel_path)
++        env.scons_dist_path = None
++        env.pythonpath = None
++        env.exe_path = env.bin_path
++        env.python_exe = relocatable_path(build_path, sys.executable)
++        env.path_utility = relocatable_path(build_path,
++                opj(rel_path, 'libtbx', 'command_line', 'path_utility.py'))
++        module_dist_paths = {}
++        for key, value in env.module_dist_paths.items():
++            head, module = os.path.split(abs(value))
++            module_dist_paths[key] = relocatable_path(build_path,
++                    opj(rel_path, module))
++        env.module_dist_paths = module_dist_paths
++        for module in env.module_list:
++            paths = []
++            for path in module.dist_paths:
++                if path != None:
++                    head, tail = os.path.split(abs(path))
++                    rp = relocatable_path(build_path, opj(rel_path, tail))
++                    paths.append(rp)
++                else:
++                    paths.append(None)
++            module.dist_paths = paths
++        _dispatcher_registry={}
++        for key, value in env._dispatcher_registry.items():
++            new_key = relocatable_path(anchor=build_path,
++                                       relocatable=key.relocatable)
++            rel = relpath(abs(value), SRCDIR)
++            new_val = relocatable_path(anchor=absolute_path(rel_path),
++                                       relocatable=rel)
++            _dispatcher_registry[new_key] = new_val
++        env._dispatcher_registry = _dispatcher_registry
++        # install the environment file in the data dir
++        file_obj = open(libtbx_env_path, 'wb')
++        pickle.dump(env, file_obj, 0)
++        file_obj.close()
++
++class clean(_clean):
++    def run(self):
++        # remove the scons build dir
++        builddir = opj(os.path.abspath(self.build_temp), 'cctbx-build')
++        if os.path.exists(builddir):
++            remove_tree(builddir, dry_run=self.dry_run)
++        else:
++            log.debug("'%s' does not exist -- can't clean it",
++                      builddir)
++        # remove the scons test dir
++        testdir = opj(os.path.abspath(self.build_temp), 'cctbx-test')
++        if os.path.exists(testdir):
++            remove_tree(testdir, dry_run=self.dry_run)
++        else:
++            log.debug("'%s' does not exist -- can't clean it",
++                      testdir)
++        # call the base class to remove the distutils dirs
++        _clean.run(self)
++
++# adapted from setuptools
++# authors: Phillip J. Eby, Tarek Ziade and the distutils SIG
++# licence: PSF or ZPL
++
++from distutils.util import convert_path
++import re
++
++EXTPAT1 = re.compile(r"^from (\S+_ext) import")
++EXTPAT2 = re.compile(r"^import (\S+_ext)$")
++EXTPAT3 = re.compile(r"boost.python.import_ext\(['\"](\S+_ext)['\"]\)$")
++EXTPAT4 = re.compile(r"import_ext\(['\"](\S+_ext)['\"]\)$")    # in module boost.python!
++
++def find_packages_and_extensions(where='.', exclude=()):
++    """Return a list all Python packages found within directory 'where'
++    and a list all extensions that need to be installed inside those packages
++
++    'where' should be supplied as a "cross-platform" (i.e. URL-style) path; it
++    will be converted to the appropriate local path syntax.  'exclude' is a
++    sequence of package names to exclude; '*' can be used as a wildcard in the
++    names, such that 'foo.*' will exclude all subpackages of 'foo' (but not
++    'foo' itself).
++    """
++    out = []
++    outext = set()
++    stack=[(convert_path(where), '')]
++
++    while stack:
++
++        where,prefix = stack.pop(0)
++        for name in os.listdir(where):
++
++            fn = opj(where,name)
++            if ('.' not in name and os.path.isdir(fn) and
++                os.path.isfile(opj(fn,'__init__.py'))
++            ):
++
++                out.append(prefix+name); stack.append((fn,prefix+name+'.'))
++
++            if name.endswith('.py'):
++
++                f = open(opj(where, name))
++                for l in f:
++
++                    m = EXTPAT1.match(l)
++                    if m is not None:
++                        outext.add(m.group(1))
++
++                    m = EXTPAT2.match(l)
++                    if m is not None:
++                        outext.add(m.group(1))
++
++                    m = EXTPAT3.search(l)
++                    if m is not None:
++                        outext.add(m.group(1))
++
++                    if name == 'python.py' and prefix.endswith('boost.'):
++                        m = EXTPAT4.search(l)
++                        if m is not None:
++                            outext.add(m.group(1))
++
++                f.close()
++
++    for pat in list(exclude)+['ez_setup', 'distribute_setup']:
++        from fnmatch import fnmatchcase
++        out = [item for item in out if not fnmatchcase(item,pat)]
++
++    return out, list(outext)
+diff --git a/setup.py b/setup.py
+new file mode 100755
+index 0000000..033dc9e
+--- /dev/null
++++ b/setup.py
+@@ -0,0 +1,142 @@
++from distutils.core import setup, Extension
++import sys, os, shutil
++
++# General settings
++opj = os.path.join
++CURDIR = os.getcwd()
++SRCDIR = opj(CURDIR, 'cctbx_sources')
++py_vers = sys.version_info
++py_major = py_vers[0]
++py_minor = py_vers[1]
++py_str = 'python%s.%s'%(py_major, py_minor)
++clipper = opj('clipper_adaptbx','clipper')
++boost = opj('boost_adaptbx','boost')
++libtbx_pypath = opj('libtbx','pythonpath')
++scons_exe = '/usr/bin/scons'    # FIXME platform dependent path
++scons_path = '/usr/lib/scons/'
++PATHLIST= [ SRCDIR,
++            opj(SRCDIR, libtbx_pypath),
++            opj(SRCDIR, clipper),
++            opj(SRCDIR, boost),
++            scons_path,
++          ]
++for p in PATHLIST:
++    if p not in sys.path:
++        # we need to insert at the front, in case cctbx is already installed
++        sys.path.insert(0,p)
++
++import sconsutils
++from sconsutils import find_packages_and_extensions, build_ext, build_py, test, install_lib, install_data, clean
++
++sconsutils.SRCDIR = SRCDIR
++
++# Debian Multiarch magic
++multiarch = os.environ.get('DEB_HOST_MULTIARCH')
++libdir = os.environ.get('MULTILIBDIR')
++if multiarch == None:
++    multiarch = ''
++else:
++    libdir = 'lib/' + multiarch
++
++if libdir == None:
++    libdir = 'lib'
++# Configure settings
++# We need this directory to get env_config.cold_start to run!
++# trailing slash is important
++init_dir = opj(SRCDIR, 'libtbx')+os.sep    # the separator is needed for dirname to do the right thing
++build_opts = [ '--libtoolize',
++               '--use_system_libs',
++               '--use-environment-flags',
++               '--libdir', libdir,
++               '--install_prefix', '%PREFIX%',    # prefix will be replaced at run time
++             ]
++conf_modules = [ 'annlib_adaptbx',
++                 'boost_adaptbx',
++                 'cbflib_adaptbx',
++                 'ccp4io_adaptbx',
++                 'cctbx',
++                 'chiltbx',
++                 'clipper_adaptbx',
++                 'crys3d',
++                 'fable',
++                 'fftw3tbx',
++                 'gltbx',
++                 'iotbx',
++                 'libtbx',
++                 'mmtbx',
++                 'omptbx',
++                 'rstbx',
++                 'scitbx',
++                 'smtbx',
++                 'spotfinder',
++                 'tbxx',
++                 'tntbx',
++                 'ucif',
++                 'wxtbx',
++               ]
++sconsutils.configure_list = [init_dir]
++sconsutils.configure_list.extend(build_opts)
++sconsutils.configure_list.extend(conf_modules)
++
++# Build settings
++sconsutils.scons_buildargv = [sys.executable, scons_exe]
++
++# Install settings
++sconsutils.scons_installargv = [sys.executable, scons_exe, 'install']
++
++# Setup settings
++
++NAME = 'cctbx'
++VERSION = '2012.05.08.2305'
++DESCRIPTION = 'cctbx'
++AUTHOR = 'cctbx'
++AUTHOR_EMAIL = 'cctbx@×××××××.gov'
++URL = 'http://cctbx.sourceforge.net/'
++LICENSE = 'CCTBX 2.0'
++KEYWORDS = 'crystallography'
++SCRIPTS = []
++PKG_DATA = {}
++EXTRA_PATH = 'cctbx'
++
++MODS = ['stdlib']
++
++PACKDIR = { 'boost' : 'cctbx_sources/boost_adaptbx/boost',    # in setup, paths must stay in unix syntax
++            'clipper' : 'cctbx_sources/clipper_adaptbx/clipper',    # also, let's keep them relative
++            'optik' : 'cctbx_sources/libtbx/pythonpath/optik',    # FIXME installs incompatible fork to global path
++            'tntbx' : 'cctbx_sources/tntbx/tntbx',
++            '' : 'cctbx_sources',
++          }
++
++PACKS = []
++EXT_MODULES = []
++for key, value in PACKDIR.items():
++    p, e = find_packages_and_extensions(value)
++    PACKS.extend(p)
++    EXT_MODULES.extend(e)
++    if key != '':
++        PACKS.append(key)
++
++EXT_MODULES = [ Extension(e, ['%SCONSLIB%']) for e in EXT_MODULES ]    # special treatment from install_lib
++
++setup(name=NAME,
++      version = VERSION,
++      author = AUTHOR,
++      author_email = AUTHOR_EMAIL,
++      url = URL,
++      description = DESCRIPTION,
++      license = LICENSE,
++      keywords = KEYWORDS,
++      extra_path = EXTRA_PATH,
++      scripts = SCRIPTS,
++      py_modules = MODS,
++      package_dir = PACKDIR,
++      packages = PACKS,
++      ext_modules = EXT_MODULES,
++      data_files = [('share/cctbx/%s'%(py_str), ['%LIBTBXENV%'])],    # special treatment from install_data
++      cmdclass = {'build_ext': build_ext,
++                  'build_py': build_py,
++                  'test': test,
++                  'install_lib': install_lib,
++                  'install_data': install_data,
++                  'clean': clean},
++     )

diff --git a/sci-libs/cctbx/files/2013.02.27.0005/0011-fix-missing-python-lib-during-linking.patch b/sci-libs/cctbx/files/2013.02.27.0005/0011-fix-missing-python-lib-during-linking.patch
new file mode 100644
index 0000000..6724c0c
--- /dev/null
+++ b/sci-libs/cctbx/files/2013.02.27.0005/0011-fix-missing-python-lib-during-linking.patch
@@ -0,0 +1,47 @@
+From: Radostan Riedel <raybuntu@××××××××××.com>
+Date: Thu, 19 Jul 2012 23:26:30 +0200
+Subject: fix missing python lib during linking
+
+---
+ cctbx_sources/libtbx/SConscript              |    4 ++--
+ cctbx_sources/scitbx/boost_python/SConscript |    2 +-
+ 2 files changed, 3 insertions(+), 3 deletions(-)
+
+diff --git a/cctbx_sources/libtbx/SConscript b/cctbx_sources/libtbx/SConscript
+index 58bdd30..53e1512 100644
+--- a/cctbx_sources/libtbx/SConscript
++++ b/cctbx_sources/libtbx/SConscript
+@@ -54,9 +54,11 @@ def set_python_include_and_libs(env_etc):
+   env_etc.python_include = libtbx.env_config.python_include_path()
+   if (sys.platform == "win32"):
+     env_etc.libs_python = ["python" + sys.version[0] + sys.version[2]]
++    env_etc.py_lib = 'python%s%s'%(sys.version[0], sys.version[2])
+     env_etc.libpath_python = [sys.prefix + r"\libs"]
+   else:
+     env_etc.libs_python = []
++    env_etc.py_lib = 'python%s.%s'%(sys.version[0], sys.version[2])
+     env_etc.libpath_python = []
+   if (env_etc.compiler.startswith("darwin_")):
+     env_etc.python_framework = "/".join(
+@@ -1034,8 +1036,6 @@ def check_syslib(lib, extra_libs=None):
+     return True
+ env_etc.check_syslib = check_syslib
+ 
+-env_etc.py_lib = 'python%s.%s'%(sys.version[0], sys.version[2])
+-
+ if (libtbx.env.build_options.use_system_libs):
+   env_etc.use_system_libs = True
+ 
+diff --git a/cctbx_sources/scitbx/boost_python/SConscript b/cctbx_sources/scitbx/boost_python/SConscript
+index 1f396e5..b906eb3 100644
+--- a/cctbx_sources/scitbx/boost_python/SConscript
++++ b/cctbx_sources/scitbx/boost_python/SConscript
+@@ -7,7 +7,7 @@ env_etc.enable_more_warnings(env=env)
+ env.Append(CXXFLAGS=env_etc.cxxflags_bpl_defines_base)
+ env.Append(SHCXXFLAGS=env_etc.cxxflags_bpl_defines_base)
+ env.Append(LIBPATH=env_etc.libpath_python)
+-env.Append(LIBS=[env_etc.boost_python] + env_etc.libs_python)
++env.Append(LIBS=[env_etc.boost_python] + [env_etc.py_lib,] + env_etc.libs_python)
+ env_etc.include_registry.append(
+   env=env,
+   paths=env_etc.scitbx_common_includes + [env_etc.python_include])

diff --git a/sci-libs/cctbx/files/2013.02.27.0005/0012-fix-to-remove-cctbx.python-interpreter.patch b/sci-libs/cctbx/files/2013.02.27.0005/0012-fix-to-remove-cctbx.python-interpreter.patch
new file mode 100644
index 0000000..6fad24f
--- /dev/null
+++ b/sci-libs/cctbx/files/2013.02.27.0005/0012-fix-to-remove-cctbx.python-interpreter.patch
@@ -0,0 +1,20 @@
+From: Radostan Riedel <raybuntu@××××××××××.com>
+Date: Mon, 23 Jul 2012 23:58:46 +0200
+Subject: fix to remove cctbx.python interpreter
+
+---
+ cctbx_sources/rstbx/bpcx/uc1_2.py       |    2 +-
+ cctbx_sources/rstbx/bpcx/uc1_2_reeke.py |    2 +-
+ 2 files changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/cctbx_sources/rstbx/bpcx/uc1_2.py b/cctbx_sources/rstbx/bpcx/uc1_2.py
+index 95ee9cd..1abf8e1 100644
+--- a/cctbx_sources/rstbx/bpcx/uc1_2.py
++++ b/cctbx_sources/rstbx/bpcx/uc1_2.py
+@@ -1,5 +1,5 @@
+ from __future__ import division
+-#!/usr/bin/env cctbx.python
++#!/usr/bin/env python
+ #
+ # Biostruct-X Data Reduction Use Case 1.2:
+ #

diff --git a/sci-libs/cctbx/files/2013.02.27.0005/0013-fix-to-support-LDFLAGS-in-use_enviroment_flags.patch b/sci-libs/cctbx/files/2013.02.27.0005/0013-fix-to-support-LDFLAGS-in-use_enviroment_flags.patch
new file mode 100644
index 0000000..8243d93
--- /dev/null
+++ b/sci-libs/cctbx/files/2013.02.27.0005/0013-fix-to-support-LDFLAGS-in-use_enviroment_flags.patch
@@ -0,0 +1,90 @@
+From: Radostan Riedel <raybuntu@××××××××××.com>
+Date: Tue, 24 Jul 2012 17:12:30 +0200
+Subject: fix to support LDFLAGS in use_enviroment_flags
+
+---
+ cctbx_sources/libtbx/SConscript    |   11 ++++++++++-
+ cctbx_sources/libtbx/env_config.py |    7 ++++++-
+ 2 files changed, 16 insertions(+), 2 deletions(-)
+
+diff --git a/cctbx_sources/libtbx/SConscript b/cctbx_sources/libtbx/SConscript
+index 53e1512..7d51d4a 100644
+--- a/cctbx_sources/libtbx/SConscript
++++ b/cctbx_sources/libtbx/SConscript
+@@ -777,11 +777,15 @@ else:
+   # user options for any compiler from the environment variables
+   # at the time of configure
+   opts = libtbx.env.build_options
++  env_etc.ldflags_base = []
+   if( opts.use_environment_flags ):
+     print "libtbx.scons: using flags from initial environment: "
+     print "              CXXFLAGS = ", opts.env_cxxflags
+     print "              CFLAGS = ", opts.env_cflags
+     print "              CPPFLAGS = ", opts.env_cppflags
++    print "              LDFLAGS = ", opts.env_ldflags
++    flg = opts.env_ldflags.split(" ")
++    env_etc.ldflags_base = flg
+     flg = opts.env_cxxflags.split(" ")
+     if( hasattr(env_etc, "cxxflags_base") ):
+       env_etc.cxxflags_base.extend(flg)
+@@ -853,6 +857,9 @@ def env_base_sync_with_env_etc():
+     SHCFLAGS=env_etc.cflags_base,
+     SHCCFLAGS=env_etc.ccflags_base,
+     SHCXXFLAGS=env_etc.cxxflags_base)
++  env_base.Prepend(LINKFLAGS=env_etc.ldflags_base)
++  env_etc.shlinkflags.extend(env_etc.ldflags_base)
++  env_etc.shlinkflags_bpl.extend(env_etc.ldflags_base)
+ env_base_sync_with_env_etc()
+ 
+ if (static_exe):
+@@ -1070,8 +1077,10 @@ def set_libtool(env):
+   # for reference. Otherwise it will be set to 0:0:0
+   env_etc.shobjsuffix_save = env['SHOBJSUFFIX']
+   env_etc.SharedLibBuilder_save = env['BUILDERS']['SharedLibrary']
++  sh_flg = list(env_etc.ldflags_base)
++  sh_flg.extend(['-rpath', env_etc.rpath])
+   env.Replace(
+-    SHLINKFLAGS='-rpath ' + env_etc.rpath,
++    SHLINKFLAGS=sh_flg,
+     SHOBJSUFFIX='.lo',
+     SHLIBSUFFIX='.la',
+   )
+diff --git a/cctbx_sources/libtbx/env_config.py b/cctbx_sources/libtbx/env_config.py
+index 3d9133e..d8fb063 100644
+--- a/cctbx_sources/libtbx/env_config.py
++++ b/cctbx_sources/libtbx/env_config.py
+@@ -1803,6 +1803,7 @@ class build_options:
+       self.env_cxxflags = ""
+       self.env_cflags = ""
+       self.env_cppflags = ""
++      self.env_ldflags = ""
+       flg = os.environ.get("CXXFLAGS")
+       if flg is not None:
+         self.env_cxxflags = flg
+@@ -1812,6 +1813,9 @@ class build_options:
+       flg = os.environ.get("CPPFLAGS")
+       if flg is not None:
+         self.env_cppflags = flg
++      flg = os.environ.get("LDFLAGS")
++      if flg is not None:
++        self.env_ldflags = flg
+ 
+   def report(self, f=None):
+     if (f is None): f = sys.stdout
+@@ -1843,6 +1847,7 @@ class build_options:
+       print >>f, "  CXXFLAGS = ", self.env_cxxflags
+       print >>f, "  CFLAGS = ", self.env_cflags
+       print >>f, "  CPPFLAGS = ", self.env_cppflags
++      print >>f, "  LDFLAGS = ", self.env_ldflags
+ 
+ class include_registry:
+ 
+@@ -2000,7 +2005,7 @@ class pre_process_args:
+         action="store_true",
+         default=False,
+         help="add compiler flags from environment variables: CXXFLAGS, CFLAGS,"
+-             " CPPFLAGS")
++             " CPPFLAGS, LDFLAGS")
+       parser.option(None, "--force_32bit",
+         action="store_true",
+         default=False,

diff --git a/sci-libs/cctbx/files/2013.02.27.0005/0014-Fix-to-append-CPPFLAGS-to-CXXFLAGS.patch b/sci-libs/cctbx/files/2013.02.27.0005/0014-Fix-to-append-CPPFLAGS-to-CXXFLAGS.patch
new file mode 100644
index 0000000..c3e357e
--- /dev/null
+++ b/sci-libs/cctbx/files/2013.02.27.0005/0014-Fix-to-append-CPPFLAGS-to-CXXFLAGS.patch
@@ -0,0 +1,21 @@
+From: Radostan Riedel <raybuntu@××××××××××.com>
+Date: Wed, 25 Jul 2012 01:44:36 +0200
+Subject: Fix to append CPPFLAGS to CXXFLAGS.
+
+---
+ cctbx_sources/libtbx/SConscript |    2 ++
+ 1 file changed, 2 insertions(+)
+
+diff --git a/cctbx_sources/libtbx/SConscript b/cctbx_sources/libtbx/SConscript
+index 7d51d4a..11a7810 100644
+--- a/cctbx_sources/libtbx/SConscript
++++ b/cctbx_sources/libtbx/SConscript
+@@ -798,6 +798,8 @@ else:
+       env_etc.ccflags_base = flg
+     flg = opts.env_cppflags.split(" ")
+     env_etc.ccflags_base.extend(flg)
++    # Need to append CPPFLAGS to cxxflags_base too!
++    env_etc.cxxflags_base.extend(flg)
+ 
+ """ ************************ Custom Builders and Emitters ********************************* """
+ 

diff --git a/sci-libs/cctbx/files/2013.02.27.0005/0016-autogenerate-pkgconfig-files.patch b/sci-libs/cctbx/files/2013.02.27.0005/0016-autogenerate-pkgconfig-files.patch
new file mode 100644
index 0000000..e3ba655
--- /dev/null
+++ b/sci-libs/cctbx/files/2013.02.27.0005/0016-autogenerate-pkgconfig-files.patch
@@ -0,0 +1,305 @@
+From: Radostan Riedel <raybuntu@××××××××××.com>
+Date: Mon, 6 Aug 2012 13:50:30 +0200
+Subject: autogenerate pkgconfig files
+
+---
+ cctbx_sources/cctbx/SConscript                     |    7 ++--
+ .../cctbx/sgtbx/direct_space_asu/proto/SConscript  |    5 ++-
+ cctbx_sources/iotbx/mtz/SConscript                 |    6 +++-
+ cctbx_sources/iotbx/pdb/SConscript                 |    5 ++-
+ cctbx_sources/libtbx/SConscript                    |   37 +++++++++++++++++++-
+ cctbx_sources/mmtbx/masks/SConscript               |    5 ++-
+ cctbx_sources/omptbx/SConscript                    |    5 ++-
+ cctbx_sources/rstbx/SConscript                     |    5 ++-
+ cctbx_sources/scitbx/boost_python/SConscript       |    5 ++-
+ cctbx_sources/scitbx/minpack/SConscript            |    5 ++-
+ cctbx_sources/scitbx/slatec/SConscript             |    5 ++-
+ .../smtbx/refinement/constraints/SConscript        |    5 ++-
+ cctbx_sources/spotfinder/SConscript                |    5 ++-
+ 13 files changed, 86 insertions(+), 14 deletions(-)
+
+diff --git a/cctbx_sources/cctbx/SConscript b/cctbx_sources/cctbx/SConscript
+index 6ce770c..378cb36 100644
+--- a/cctbx_sources/cctbx/SConscript
++++ b/cctbx_sources/cctbx/SConscript
+@@ -96,9 +96,12 @@ lib_cctbx_sources = [
+ ]
+ if (env_etc.static_libraries): builder = envlm.StaticLibrary
+ else:                          builder = envlm.SharedLibrary
++name='cctbx'
+ builder(
+-  target="#lib/cctbx",
+-  source=lib_cctbx_sources)
++        target="#lib/"+name,
++        source=lib_cctbx_sources)
++desc='Library for general crystallographic applications'
++env_etc.create_pc_file(name=name, version='0.0.0', desc=desc)
+ 
+ SConscript("examples/SConscript")
+ 
+diff --git a/cctbx_sources/cctbx/sgtbx/direct_space_asu/proto/SConscript b/cctbx_sources/cctbx/sgtbx/direct_space_asu/proto/SConscript
+index 5a5cfbd..4328794 100644
+--- a/cctbx_sources/cctbx/sgtbx/direct_space_asu/proto/SConscript
++++ b/cctbx_sources/cctbx/sgtbx/direct_space_asu/proto/SConscript
+@@ -16,9 +16,12 @@ lib_asu_sources = [
+ if (env_etc.static_libraries): builder = env.StaticLibrary
+ else:                          builder = env.SharedLibrary
+ 
++name='cctbx_sgtbx_asu'
+ builder(
+-  target="#lib/cctbx_sgtbx_asu",
++  target="#lib/"+name,
+   source=lib_asu_sources)
++desc='Direct space asymmetric unit class library'
++env_etc.create_pc_file(name=name, version='0.0.0', desc=desc)
+ 
+ env = env.Clone()
+ env.Prepend(LIBS=["cctbx_sgtbx_asu"])
+diff --git a/cctbx_sources/iotbx/mtz/SConscript b/cctbx_sources/iotbx/mtz/SConscript
+index cd539e6..f7d22b8 100644
+--- a/cctbx_sources/iotbx/mtz/SConscript
++++ b/cctbx_sources/iotbx/mtz/SConscript
+@@ -9,13 +9,17 @@ env.Append(SHCXXFLAGS=env_etc.ccp4io_defines)
+ env_etc.enable_more_warnings(env=env)
+ if (env_etc.static_libraries): builder = env.StaticLibrary
+ else:                          builder = env.SharedLibrary
++name='iotbx_mtz'
+ builder(
+-  target="#lib/iotbx_mtz",
++  target="#lib/"+name,
+   source=[
+     "object.cpp",
+     "crystal.cpp",
+     "dataset.cpp",
+     "column.cpp"])
++desc='Wrapper Library to work with CCP4 MTZ files'
++env_etc.create_pc_file(name=name, version='0.0.0', desc=desc)
++
+ 
+ if (not env_etc.no_boost_python):
+   Import("env_iotbx_boost_python_ext")
+diff --git a/cctbx_sources/iotbx/pdb/SConscript b/cctbx_sources/iotbx/pdb/SConscript
+index 9b89fe1..8a83058 100644
+--- a/cctbx_sources/iotbx/pdb/SConscript
++++ b/cctbx_sources/iotbx/pdb/SConscript
+@@ -9,8 +9,9 @@ env_etc.include_registry.append(
+   paths=env_etc.iotbx_common_includes)
+ if (env_etc.static_libraries): builder = env.StaticLibrary
+ else:                          builder = env.SharedLibrary
++name='iotbx_pdb'
+ builder(
+-  target="#lib/iotbx_pdb",
++  target="#lib/"+name,
+   source=[
+     "hybrid_36_c.c",
+     "hybrid_36_cpp.cpp",
+@@ -25,6 +26,8 @@ builder(
+     "atom_selection.cpp",
+     "input.cpp",
+     "input_write.cpp"])
++desc='Fast comprehensive PDB handling library'
++env_etc.create_pc_file(name=name, version='0.0.0', desc=desc)
+ 
+ env = env.Clone()
+ env_etc.include_registry.append(env=env, paths=[env_etc.fable_include])
+diff --git a/cctbx_sources/libtbx/SConscript b/cctbx_sources/libtbx/SConscript
+index 11a7810..1e91202 100644
+--- a/cctbx_sources/libtbx/SConscript
++++ b/cctbx_sources/libtbx/SConscript
+@@ -1070,8 +1070,34 @@ env_etc.install_path = os.path.abspath(env_etc.destdir + '/' + env_etc.prefix)
+ env_etc.binpath = os.path.join(env_etc.install_path, 'bin')
+ env_etc.libpath = os.path.abspath(env_etc.install_path + '/' + env_etc.libdir)
+ env_etc.inclpath = os.path.join(env_etc.install_path, 'include')
++env_etc.pkgpath = os.path.join(env_etc.install_path, 'lib/pkgconfig')
+ env_etc.rpath = os.path.abspath(env_etc.prefix + '/' + env_etc.libdir)
+ 
++def create_pc_file(name, version, desc, requires=None, requires_private=None,
++                   conflicts=None, libs_private=None):
++  """ Create pkg-config file. """
++  fpath = '%s/%s.pc'%(abs(libtbx.env.lib_path), name)
++  pc = open(fpath, 'w')
++  pc.write('prefix=%s\n'%env_etc.prefix)
++  pc.write('exec_prefix=${prefix}\n')
++  pc.write('libdir=${prefix}/%s\n'%env_etc.libdir)
++  pc.write('includedir=${prefix}/include\n\n')
++  pc.write('Name: %s\n'%name)
++  pc.write('Description: %s\n'%desc)
++  pc.write('Version: %s\n'%version)
++  if requires != None:
++    pc.write('Requires: %s\n'%requires)
++  if requires_private != None:
++    pc.write('Requires.private: %s\n'%requires_private)
++  if conflicts != None:
++    pc.write('Conflicts: %s\n'%conflicts)
++  pc.write('Libs: -L${libdir} -l%s\n'%name)
++  if libs_private != None:
++    pc.write('Libs.private: %s\n'%libs_private)
++  pc.write('Cflags: -I${includedir}')
++  pc.close()
++env_etc.create_pc_file = create_pc_file
++
+ def set_libtool(env):
+   # Versioning can be provided by appending "-version-info 3:12:1" to SHLINKFLAGS
+   # Please see:
+@@ -1197,6 +1223,11 @@ def create_install_targets():
+           src = os.path.join(src_dir, root, filename)
+           env_base.Install(dest, src)
+           env_base.Alias("install-header", dest)
++        if re.match('^.*\.pc$', filename, flags=re.IGNORECASE):
++          dest = os.path.join(env_etc.pkgpath, root)
++          src = os.path.join(src_dir, root, filename)
++          env_base.Install(dest, src)
++          env_base.Alias("install-pkgconfig", dest)
+       if src_dir == lib_dir:
+         break
+ 
+@@ -1204,7 +1235,11 @@ def create_install_targets():
+   dest = env_etc.binpath
+   env_base.Install(dest, Glob('%s/*'%(exe_dev)))
+   env_base.Alias("install-bin", dest)
+-  Alias('install', ['install-header', 'install-shlib', 'install-bin'])
++  Alias('install', ['install-header',
++                    'install-shlib',
++                    'install-bin',
++                    'install-pkgconfig',
++                   ])
+   os.chdir(cwd)
+ 
+ if 'install' in COMMAND_LINE_TARGETS:
+diff --git a/cctbx_sources/mmtbx/masks/SConscript b/cctbx_sources/mmtbx/masks/SConscript
+index ef93088..a6187cc 100644
+--- a/cctbx_sources/mmtbx/masks/SConscript
++++ b/cctbx_sources/mmtbx/masks/SConscript
+@@ -13,9 +13,12 @@ lib_sources = [
+ if (env_etc.static_libraries): builder = env.StaticLibrary
+ else:                          builder = env.SharedLibrary
+ 
++name='mmtbx_masks'
+ builder(
+-  target="#lib/mmtbx_masks",
++  target="#lib/"+name,
+   source=lib_sources)
++desc='Masks for bulk solvent modelling'
++env_etc.create_pc_file(name=name, version='0.0.0', desc=desc)
+ 
+ env = env.Clone()
+ env.Prepend(LIBS=["mmtbx_masks", "iotbx_pdb"])
+diff --git a/cctbx_sources/omptbx/SConscript b/cctbx_sources/omptbx/SConscript
+index 43aac91..76bb923 100644
+--- a/cctbx_sources/omptbx/SConscript
++++ b/cctbx_sources/omptbx/SConscript
+@@ -12,9 +12,12 @@ env_etc.include_registry.append(
+   paths=[env_etc.omptbx_include])
+ if (env_etc.static_libraries): builder = env.StaticLibrary
+ else:                          builder = env.SharedLibrary
++name='omptbx'
+ builder(
+-  target="#lib/omptbx",
++  target="#lib/"+name,
+   source=["stubs.cpp"])
++desc='OpenMP interface for CCTBX'
++env_etc.create_pc_file(name=name, version='0.0.0', desc=desc)
+ 
+ if (not env_etc.no_boost_python):
+   Import("env_boost_python_ext")
+diff --git a/cctbx_sources/rstbx/SConscript b/cctbx_sources/rstbx/SConscript
+index e2958a1..6d66476 100644
+--- a/cctbx_sources/rstbx/SConscript
++++ b/cctbx_sources/rstbx/SConscript
+@@ -26,14 +26,17 @@ env_etc.include_registry.append(
+   paths=env_etc.rstbx_common_includes)
+ if (env_etc.static_libraries): builder = env.StaticLibrary
+ else:                          builder = env.SharedLibrary
++name='rstbx'
+ builder(
+-  target="#lib/rstbx",
++  target="#lib/"+name,
+   source=["dps_core/dps_core.cpp",
+           "dps_core/directional_fft.cpp",
+           "dps_core/direction.cpp",
+           "diffraction/ewald_sphere.cpp",
+           "diffraction/partial_spot_position_partial_H.cpp"
+   ])
++desc='Library for calculations in reciprocal space'
++env_etc.create_pc_file(name=name, version='0.0.0', desc=desc)
+ 
+ if (not env_etc.no_boost_python):
+   Import("env_boost_python_ext")
+diff --git a/cctbx_sources/scitbx/boost_python/SConscript b/cctbx_sources/scitbx/boost_python/SConscript
+index b906eb3..0b81d9a 100644
+--- a/cctbx_sources/scitbx/boost_python/SConscript
++++ b/cctbx_sources/scitbx/boost_python/SConscript
+@@ -19,6 +19,9 @@ lib_scitbx_boost_python_sources = [
+ ]
+ if (env_etc.static_libraries): builder = env.StaticLibrary
+ else:                          builder = env.SharedLibrary
++name=env_etc.scitbx_boost_python
+ builder(
+-  target="#lib/%s"%env_etc.scitbx_boost_python,
++  target="#lib/"+name,
+   source=lib_scitbx_boost_python_sources)
++desc='#TODO'
++env_etc.create_pc_file(name=name, version='0.0.0', desc=desc)
+diff --git a/cctbx_sources/scitbx/minpack/SConscript b/cctbx_sources/scitbx/minpack/SConscript
+index 7c325cb..ee7509e 100644
+--- a/cctbx_sources/scitbx/minpack/SConscript
++++ b/cctbx_sources/scitbx/minpack/SConscript
+@@ -9,7 +9,10 @@ env_etc.include_registry.append(
+ env.Append(LIBS=env_etc.libm)
+ if (env_etc.static_libraries): builder = env.StaticLibrary
+ else:                          builder = env.SharedLibrary
+-builder(target='#lib/scitbx_minpack', source=["raw.cpp"])
++name='scitbx_minpack'
++builder(target='#lib/'+name, source=["raw.cpp"])
++desc='C++ port of files in MINPACK'
++env_etc.create_pc_file(name=name, version='0.0.0', desc=desc)
+ 
+ if (not env_etc.no_boost_python):
+   Import("env_scitbx_boost_python_ext")
+diff --git a/cctbx_sources/scitbx/slatec/SConscript b/cctbx_sources/scitbx/slatec/SConscript
+index ca9b6da..39e38e1 100644
+--- a/cctbx_sources/scitbx/slatec/SConscript
++++ b/cctbx_sources/scitbx/slatec/SConscript
+@@ -6,4 +6,7 @@ env_etc.enable_more_warnings(env=env)
+ env.Append(LIBS=env_etc.libm)
+ if (env_etc.static_libraries): builder = env.StaticLibrary
+ else:                          builder = env.SharedLibrary
+-builder(target='#lib/scitbx_slatec', source=["lib_c.c"])
++name='scitbx_slatec'
++builder(target='#lib/'+name, source=["lib_c.c"])
++desc='C port of files in SLATEC'
++env_etc.create_pc_file(name=name, version='0.0.0', desc=desc)
+diff --git a/cctbx_sources/smtbx/refinement/constraints/SConscript b/cctbx_sources/smtbx/refinement/constraints/SConscript
+index 67d99dc..306d1a4 100644
+--- a/cctbx_sources/smtbx/refinement/constraints/SConscript
++++ b/cctbx_sources/smtbx/refinement/constraints/SConscript
+@@ -4,7 +4,10 @@ env_etc.include_registry.append(env=env,
+                                 paths=["."] + env_etc.smtbx_common_includes)
+ if (env_etc.static_libraries): builder = env.StaticLibrary
+ else:                          builder = env.SharedLibrary
+-builder(target="#lib/smtbx_refinement_constraints", source=Glob("*.cpp"))
++name='smtbx_refinement_constraints'
++builder(target="#lib/"+name, source=Glob("*.cpp"))
++desc='Library for small molecule crystallography constraints'
++env_etc.create_pc_file(name=name, version='0.0.0', desc=desc)
+ 
+ env_program = env.Clone()
+ env_program.Prepend(LIBS=[ "cctbx", "smtbx_refinement_constraints" ])
+diff --git a/cctbx_sources/spotfinder/SConscript b/cctbx_sources/spotfinder/SConscript
+index 1d73677..a63c6d9 100644
+--- a/cctbx_sources/spotfinder/SConscript
++++ b/cctbx_sources/spotfinder/SConscript
+@@ -46,9 +46,12 @@ lib_spotfinder_sources = [
+ 
+ if (env_etc.static_libraries): builder = envlm.StaticLibrary
+ else:                          builder = envlm.SharedLibrary
++name='spotfinder'
+ builder(
+-    target="#lib/spotfinder",
++    target="#lib/"+name,
+     source=lib_spotfinder_sources)
++desc='Library for locating Bragg-Spots on x-ray diffraction images'
++env_etc.create_pc_file(name=name, version='0.0.0', desc=desc)
+ 
+ if (not env_etc.no_boost_python):
+   Import("env_no_includes_boost_python_ext")

diff --git a/sci-libs/cctbx/files/2013.02.27.0005/0017-Fix-to-use-systems-include-path.patch b/sci-libs/cctbx/files/2013.02.27.0005/0017-Fix-to-use-systems-include-path.patch
new file mode 100644
index 0000000..4affc54
--- /dev/null
+++ b/sci-libs/cctbx/files/2013.02.27.0005/0017-Fix-to-use-systems-include-path.patch
@@ -0,0 +1,128 @@
+From: Radostan Riedel <raybuntu@××××××××××.com>
+Date: Tue, 7 Aug 2012 18:15:43 +0200
+Subject: Fix to use systems include path
+
+---
+ .../cbflib_adaptbx/detectors/boost_python/cbf_binary_adaptor.h   |    4 ++--
+ .../cbflib_adaptbx/detectors/boost_python/general_cbf_write.h    |    4 ++--
+ cctbx_sources/cbflib_adaptbx/detectors/cbf_adaptor.h             |    4 ++--
+ .../cbflib_adaptbx/detectors/cbf_byte_offset_optimized.cpp       |    6 +++---
+ cctbx_sources/cbflib_adaptbx/detectors/tst_memory.cpp            |    4 ++--
+ cctbx_sources/ccp4io_adaptbx/ext.cpp                             |    2 +-
+ cctbx_sources/iotbx/mtz/ext.cpp                                  |    2 +-
+ cctbx_sources/iotbx/mtz/object.h                                 |    6 +++---
+ 8 files changed, 16 insertions(+), 16 deletions(-)
+
+diff --git a/cctbx_sources/cbflib_adaptbx/detectors/boost_python/cbf_binary_adaptor.h b/cctbx_sources/cbflib_adaptbx/detectors/boost_python/cbf_binary_adaptor.h
+index 66677bd..516b319 100644
+--- a/cctbx_sources/cbflib_adaptbx/detectors/boost_python/cbf_binary_adaptor.h
++++ b/cctbx_sources/cbflib_adaptbx/detectors/boost_python/cbf_binary_adaptor.h
+@@ -3,8 +3,8 @@
+ #include <cbflib_adaptbx/detectors/cbf_adaptor.h>
+ #include <cbflib_adaptbx/detectors/cbf_byte_offset_optimized.h>
+ #include <cbflib_adaptbx/detectors/buffer_based_service.h>
+-#include <include/cbf_binary.h>
+-#include <include/cbf_compress.h>
++#include <cbf/cbf_binary.h>
++#include <cbf/cbf_compress.h>
+ 
+ namespace iotbx {
+   namespace detectors {
+diff --git a/cctbx_sources/cbflib_adaptbx/detectors/boost_python/general_cbf_write.h b/cctbx_sources/cbflib_adaptbx/detectors/boost_python/general_cbf_write.h
+index c6c1afb..f45b4d1 100644
+--- a/cctbx_sources/cbflib_adaptbx/detectors/boost_python/general_cbf_write.h
++++ b/cctbx_sources/cbflib_adaptbx/detectors/boost_python/general_cbf_write.h
+@@ -1,8 +1,8 @@
+ #ifndef GENERAL_CBF_WRITE_H
+ #define GENERAL_CBF_WRITE_H
+ #include <cbflib_adaptbx/detectors/cbf_adaptor.h>
+-#include "cbf_binary.h"
+-#include "cbf_compress.h"
++#include "cbf/cbf_binary.h"
++#include "cbf/cbf_compress.h"
+ 
+ namespace iotbx {
+   namespace detectors {
+diff --git a/cctbx_sources/cbflib_adaptbx/detectors/cbf_adaptor.h b/cctbx_sources/cbflib_adaptbx/detectors/cbf_adaptor.h
+index b5cc407..3787c7b 100644
+--- a/cctbx_sources/cbflib_adaptbx/detectors/cbf_adaptor.h
++++ b/cctbx_sources/cbflib_adaptbx/detectors/cbf_adaptor.h
+@@ -8,8 +8,8 @@
+ #include <exception>
+ #include <scitbx/array_family/flex_types.h>
+ #include <scitbx/array_family/versa_matrix.h>
+-#include <include/cbf.h>
+-#include <include/cbf_simple.h>
++#include <cbf/cbf.h>
++#include <cbf/cbf_simple.h>
+ #include <cbflib_adaptbx/detectors/basic.h>
+ 
+ #undef cbf_failnez
+diff --git a/cctbx_sources/cbflib_adaptbx/detectors/cbf_byte_offset_optimized.cpp b/cctbx_sources/cbflib_adaptbx/detectors/cbf_byte_offset_optimized.cpp
+index 2edbfb5..526556f 100644
+--- a/cctbx_sources/cbflib_adaptbx/detectors/cbf_byte_offset_optimized.cpp
++++ b/cctbx_sources/cbflib_adaptbx/detectors/cbf_byte_offset_optimized.cpp
+@@ -244,9 +244,9 @@ extern "C" {
+ #include <limits.h>
+ #include <ctype.h>
+ 
+-#include "cbf.h"
+-#include "cbf_file.h"
+-#include "cbf_byte_offset.h"
++#include "cbf/cbf.h"
++#include "cbf/cbf_file.h"
++#include "cbf/cbf_byte_offset.h"
+ #include <cbflib_adaptbx/detectors/cbf_byte_offset_optimized.h>
+ 
+ /* Changes made in the byte-offset algorithm
+diff --git a/cctbx_sources/cbflib_adaptbx/detectors/tst_memory.cpp b/cctbx_sources/cbflib_adaptbx/detectors/tst_memory.cpp
+index 5f5d9b1..d121530 100644
+--- a/cctbx_sources/cbflib_adaptbx/detectors/tst_memory.cpp
++++ b/cctbx_sources/cbflib_adaptbx/detectors/tst_memory.cpp
+@@ -1,5 +1,5 @@
+-#include <include/cbf.h>
+-#include <include/cbf_simple.h>
++#include <cbf/cbf.h>
++#include <cbf/cbf_simple.h>
+ #include <cstdio>
+ #include <string>
+ #include <exception>
+diff --git a/cctbx_sources/ccp4io_adaptbx/ext.cpp b/cctbx_sources/ccp4io_adaptbx/ext.cpp
+index ce21568..e507515 100644
+--- a/cctbx_sources/ccp4io_adaptbx/ext.cpp
++++ b/cctbx_sources/ccp4io_adaptbx/ext.cpp
+@@ -1,5 +1,5 @@
+ #include <boost/python.hpp>
+-#include <mmdb_manager.h>
++#include <mmdb/mmdb_manager.h>
+ #include <ssm_align.h>
+ 
+ namespace ccp4io_adaptbx { namespace boost_python {
+diff --git a/cctbx_sources/iotbx/mtz/ext.cpp b/cctbx_sources/iotbx/mtz/ext.cpp
+index b1a0db7..6aa416a 100644
+--- a/cctbx_sources/iotbx/mtz/ext.cpp
++++ b/cctbx_sources/iotbx/mtz/ext.cpp
+@@ -1,5 +1,5 @@
+ #include <boost/python/module.hpp>
+-#include <ccp4_errno.h>
++#include <ccp4/ccp4_errno.h>
+ 
+ namespace iotbx { namespace mtz { namespace boost_python {
+ 
+diff --git a/cctbx_sources/iotbx/mtz/object.h b/cctbx_sources/iotbx/mtz/object.h
+index da35fcf..b593534 100644
+--- a/cctbx_sources/iotbx/mtz/object.h
++++ b/cctbx_sources/iotbx/mtz/object.h
+@@ -6,9 +6,9 @@
+ # include <math.h>
+ #endif
+ 
+-#include <cmtzlib.h>
+-#include <ccp4_array.h>
+-#include <ccp4_errno.h>
++#include <ccp4/cmtzlib.h>
++#include <ccp4/ccp4_array.h>
++#include <ccp4/ccp4_errno.h>
+ #include <cctbx/sgtbx/space_group.h>
+ #include <cctbx/hendrickson_lattman.h>
+ #include <boost/shared_ptr.hpp>

diff --git a/sci-libs/cctbx/files/2013.02.27.0005/0018-Fix-to-skip-build-of-clipper-examples.patch b/sci-libs/cctbx/files/2013.02.27.0005/0018-Fix-to-skip-build-of-clipper-examples.patch
new file mode 100644
index 0000000..ffd4ebb
--- /dev/null
+++ b/sci-libs/cctbx/files/2013.02.27.0005/0018-Fix-to-skip-build-of-clipper-examples.patch
@@ -0,0 +1,52 @@
+From: Radostan Riedel <raybuntu@××××××××××.com>
+Date: Tue, 7 Aug 2012 18:19:02 +0200
+Subject: Fix to skip build of clipper examples
+
+---
+ cctbx_sources/clipper_adaptbx/SConscript |   33 +++++++++++++++---------------
+ 1 file changed, 17 insertions(+), 16 deletions(-)
+
+diff --git a/cctbx_sources/clipper_adaptbx/SConscript b/cctbx_sources/clipper_adaptbx/SConscript
+index c39047f..b0699ad 100644
+--- a/cctbx_sources/clipper_adaptbx/SConscript
++++ b/cctbx_sources/clipper_adaptbx/SConscript
+@@ -61,22 +61,23 @@ else:
+ env_exe = env.Clone()
+ env_exe.Prepend(LIBS=[env_etc.clipper_libs[0]])
+ 
+-exe = env_exe.Program(
+-  target='#exe_dev/'+env["PROGPREFIX"]+'clipper.symtest'
+-                    +env["PROGSUFFIX"],
+-  source = ["../clipper/examples/symtest.cpp",
+-           ])
+-libtbx.env.write_dispatcher_in_bin(
+-  source_file=exe[0].get_abspath(),
+-  target_file="clipper.symtest")
+-exe = env_exe.Program(
+-  target='#exe_dev/'+env["PROGPREFIX"]+'clipper.sanity_check'
+-                    +env["PROGSUFFIX"],
+-  source = ["sanity_check.cpp",
+-           ])
+-libtbx.env.write_dispatcher_in_bin(
+-  source_file=exe[0].get_abspath(),
+-  target_file="clipper.sanity_check")
++# Skip building clipper examples in Debian
++#exe = env_exe.Program(
++#  target='#exe_dev/'+env["PROGPREFIX"]+'clipper.symtest'
++#                    +env["PROGSUFFIX"],
++#  source = ["../clipper/examples/symtest.cpp",
++#           ])
++#libtbx.env.write_dispatcher_in_bin(
++#  source_file=exe[0].get_abspath(),
++#  target_file="clipper.symtest")
++#exe = env_exe.Program(
++#  target='#exe_dev/'+env["PROGPREFIX"]+'clipper.sanity_check'
++#                    +env["PROGSUFFIX"],
++#  source = ["sanity_check.cpp",
++#           ])
++#libtbx.env.write_dispatcher_in_bin(
++#  source_file=exe[0].get_abspath(),
++#  target_file="clipper.sanity_check")
+ 
+ if (hasattr(env_etc, "cctbx_include")):
+   if (not env_etc.no_boost_python):

diff --git a/sci-libs/cctbx/files/2013.02.27.0005/0101-system-cbf.patch b/sci-libs/cctbx/files/2013.02.27.0005/0101-system-cbf.patch
new file mode 100644
index 0000000..1688026
--- /dev/null
+++ b/sci-libs/cctbx/files/2013.02.27.0005/0101-system-cbf.patch
@@ -0,0 +1,16 @@
+ cctbx_sources/cbflib_adaptbx/detectors/cbf_byte_offset_optimized.h | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/cctbx_sources/cbflib_adaptbx/detectors/cbf_byte_offset_optimized.h b/cctbx_sources/cbflib_adaptbx/detectors/cbf_byte_offset_optimized.h
+index 0089325..02234d1 100644
+--- a/cctbx_sources/cbflib_adaptbx/detectors/cbf_byte_offset_optimized.h
++++ b/cctbx_sources/cbflib_adaptbx/detectors/cbf_byte_offset_optimized.h
+@@ -5,7 +5,7 @@
+ extern "C" {
+ #endif
+ #include <stdio.h>
+-#include <include/cbf_file.h>
++#include <cbf/cbf_file.h>
+ 
+   /* Decompress an array with the byte-offset algorithm */
+ 

diff --git a/sci-libs/cctbx/files/2013.02.27.0005/0101-system-clipper.patch b/sci-libs/cctbx/files/2013.02.27.0005/0101-system-clipper.patch
new file mode 100644
index 0000000..6f50e5f
--- /dev/null
+++ b/sci-libs/cctbx/files/2013.02.27.0005/0101-system-clipper.patch
@@ -0,0 +1,185 @@
+ cctbx_sources/clipper/clipper/cctbx/clipper_cctbx.h        |  2 +-
+ cctbx_sources/clipper/clipper/contrib/Makefile.dep         | 14 +++++++-------
+ cctbx_sources/clipper/clipper/contrib/edcalc.cpp           |  2 +-
+ cctbx_sources/clipper/clipper/contrib/fffear.cpp           |  2 +-
+ .../clipper/clipper/contrib/function_object_bases.h        |  6 +++---
+ cctbx_sources/clipper/clipper/contrib/sfcalc.cpp           |  2 +-
+ cctbx_sources/clipper/clipper/contrib/sfcalc_obs.cpp       |  4 ++--
+ cctbx_sources/clipper/clipper/contrib/sfweight.cpp         |  4 ++--
+ cctbx_sources/clipper/clipper/contrib/skeleton.cpp         |  2 +-
+ cctbx_sources/clipper_adaptbx/clipper/SConscript           |  1 -
+ 10 files changed, 19 insertions(+), 20 deletions(-)
+
+diff --git a/cctbx_sources/clipper/clipper/cctbx/clipper_cctbx.h b/cctbx_sources/clipper/clipper/cctbx/clipper_cctbx.h
+index bd9f7d2..079958d 100644
+--- a/cctbx_sources/clipper/clipper/cctbx/clipper_cctbx.h
++++ b/cctbx_sources/clipper/clipper/cctbx/clipper_cctbx.h
+@@ -47,7 +47,7 @@
+ #define CLIPPER_CCTBX
+ 
+ 
+-#include "../core/hkl_datatypes.h"
++#include "clipper/core/hkl_datatypes.h"
+ 
+ #include <cctbx/sgtbx/space_group.h>
+ #include <cctbx/hendrickson_lattman.h>
+diff --git a/cctbx_sources/clipper/clipper/contrib/Makefile.dep b/cctbx_sources/clipper/clipper/contrib/Makefile.dep
+index 98251b1..0fe7bb3 100644
+--- a/cctbx_sources/clipper/clipper/contrib/Makefile.dep
++++ b/cctbx_sources/clipper/clipper/contrib/Makefile.dep
+@@ -1,27 +1,27 @@
+ 
+-function_object_bases.h:	../core/hkl_datatypes.h ../core/xmap.h ../core/nxmap_operator.h 
++function_object_bases.h:	clipper/core/hkl_datatypes.h clipper/core/xmap.h clipper/core/nxmap_operator.h 
+ 
+ function_object_bases.o:	function_object_bases.cpp function_object_bases.h 
+ 
+ sfcalc.h:               	function_object_bases.h 
+ 
+-sfcalc.o:               	sfcalc.cpp sfcalc.h ../core/atomsf.h 
++sfcalc.o:               	sfcalc.cpp sfcalc.h clipper/core/atomsf.h 
+ 
+ edcalc.h:               	function_object_bases.h 
+ 
+-edcalc.o:               	edcalc.cpp edcalc.h ../core/atomsf.h 
++edcalc.o:               	edcalc.cpp edcalc.h clipper/core/atomsf.h 
+ 
+ sfcalc_obs.h:           	function_object_bases.h 
+ 
+-sfcalc_obs.o:           	sfcalc_obs.cpp sfcalc_obs.h edcalc.h ../core/hkl_compute.h ../core/resol_targetfn.h 
++sfcalc_obs.o:           	sfcalc_obs.cpp sfcalc_obs.h edcalc.h clipper/core/hkl_compute.h clipper/core/resol_targetfn.h 
+ 
+ sfweight.h:             	function_object_bases.h 
+ 
+-sfweight.o:             	sfweight.cpp sfweight.h ../core/hkl_operators.h ../core/resol_targetfn.h 
++sfweight.o:             	sfweight.cpp sfweight.h clipper/core/hkl_operators.h clipper/core/resol_targetfn.h 
+ 
+ fffear.h:               	function_object_bases.h 
+ 
+-fffear.o:               	fffear.cpp fffear.h ../core/map_interp.h 
++fffear.o:               	fffear.cpp fffear.h clipper/core/map_interp.h 
+ 
+ mapfilter.h:            	function_object_bases.h 
+ 
+@@ -29,7 +29,7 @@ mapfilter.o:            	mapfilter.cpp mapfilter.h
+ 
+ skeleton.h:             	function_object_bases.h 
+ 
+-skeleton.o:             	skeleton.cpp skeleton.h ../core/map_utils.h 
++skeleton.o:             	skeleton.cpp skeleton.h clipper/core/map_utils.h 
+ 
+ originmatch.h:          	function_object_bases.h 
+ 
+diff --git a/cctbx_sources/clipper/clipper/contrib/edcalc.cpp b/cctbx_sources/clipper/clipper/contrib/edcalc.cpp
+index f5df7b2..cc031bc 100644
+--- a/cctbx_sources/clipper/clipper/contrib/edcalc.cpp
++++ b/cctbx_sources/clipper/clipper/contrib/edcalc.cpp
+@@ -43,7 +43,7 @@
+ 
+ #include "edcalc.h"
+ 
+-#include "../core/atomsf.h"
++#include "clipper/core/atomsf.h"
+ 
+ 
+ namespace clipper {
+diff --git a/cctbx_sources/clipper/clipper/contrib/fffear.cpp b/cctbx_sources/clipper/clipper/contrib/fffear.cpp
+index 9a728f7..189855a 100644
+--- a/cctbx_sources/clipper/clipper/contrib/fffear.cpp
++++ b/cctbx_sources/clipper/clipper/contrib/fffear.cpp
+@@ -42,7 +42,7 @@
+ 
+ #include "fffear.h"
+ 
+-#include "../core/map_interp.h"
++#include "clipper/core/map_interp.h"
+ 
+ 
+ namespace clipper {
+diff --git a/cctbx_sources/clipper/clipper/contrib/function_object_bases.h b/cctbx_sources/clipper/clipper/contrib/function_object_bases.h
+index e6c98c7..4a40c73 100644
+--- a/cctbx_sources/clipper/clipper/contrib/function_object_bases.h
++++ b/cctbx_sources/clipper/clipper/contrib/function_object_bases.h
+@@ -48,9 +48,9 @@
+ #define CLIPPER_FUNCTION_OBJECT_BASES
+ 
+ 
+-#include "../core/hkl_datatypes.h"
+-#include "../core/xmap.h"
+-#include "../core/nxmap_operator.h"
++#include "clipper/core/hkl_datatypes.h"
++#include "clipper/core/xmap.h"
++#include "clipper/core/nxmap_operator.h"
+ 
+ 
+ namespace clipper {
+diff --git a/cctbx_sources/clipper/clipper/contrib/sfcalc.cpp b/cctbx_sources/clipper/clipper/contrib/sfcalc.cpp
+index 48c0d9c..a3c63f0 100644
+--- a/cctbx_sources/clipper/clipper/contrib/sfcalc.cpp
++++ b/cctbx_sources/clipper/clipper/contrib/sfcalc.cpp
+@@ -43,7 +43,7 @@
+ 
+ #include "sfcalc.h"
+ 
+-#include "../core/atomsf.h"
++#include "clipper/core/atomsf.h"
+ 
+ 
+ namespace clipper {
+diff --git a/cctbx_sources/clipper/clipper/contrib/sfcalc_obs.cpp b/cctbx_sources/clipper/clipper/contrib/sfcalc_obs.cpp
+old mode 100755
+new mode 100644
+index de47e09..0f67585
+--- a/cctbx_sources/clipper/clipper/contrib/sfcalc_obs.cpp
++++ b/cctbx_sources/clipper/clipper/contrib/sfcalc_obs.cpp
+@@ -43,8 +43,8 @@
+ 
+ #include "sfcalc_obs.h"
+ #include "edcalc.h"
+-#include "../core/hkl_compute.h"
+-#include "../core/resol_targetfn.h"
++#include "clipper/core/hkl_compute.h"
++#include "clipper/core/resol_targetfn.h"
+ 
+ 
+ namespace clipper {
+diff --git a/cctbx_sources/clipper/clipper/contrib/sfweight.cpp b/cctbx_sources/clipper/clipper/contrib/sfweight.cpp
+old mode 100755
+new mode 100644
+index 1b2d4dc..6ec98c2
+--- a/cctbx_sources/clipper/clipper/contrib/sfweight.cpp
++++ b/cctbx_sources/clipper/clipper/contrib/sfweight.cpp
+@@ -42,8 +42,8 @@
+ 
+ 
+ #include "sfweight.h"
+-#include "../core/hkl_operators.h"
+-#include "../core/resol_targetfn.h"
++#include "clipper/core/hkl_operators.h"
++#include "clipper/core/resol_targetfn.h"
+ 
+ 
+ namespace clipper {
+diff --git a/cctbx_sources/clipper/clipper/contrib/skeleton.cpp b/cctbx_sources/clipper/clipper/contrib/skeleton.cpp
+index bff1049..14ebf55 100644
+--- a/cctbx_sources/clipper/clipper/contrib/skeleton.cpp
++++ b/cctbx_sources/clipper/clipper/contrib/skeleton.cpp
+@@ -42,7 +42,7 @@
+ 
+ #include "skeleton.h"
+ 
+-#include "../core/map_utils.h"
++#include "clipper/core/map_utils.h"
+ 
+ 
+ namespace clipper {
+diff --git a/cctbx_sources/clipper_adaptbx/clipper/SConscript b/cctbx_sources/clipper_adaptbx/clipper/SConscript
+index 1911eb1..df03808 100644
+--- a/cctbx_sources/clipper_adaptbx/clipper/SConscript
++++ b/cctbx_sources/clipper_adaptbx/clipper/SConscript
+@@ -11,5 +11,4 @@ env.SharedLibrary(
+     "clipper_ext.cpp",
+     "hendrickson_lattman_bpl.cpp",
+     "sigmaa_bpl.cpp",
+-    "../../clipper/clipper/contrib/sfweight.cpp",
+     "../../clipper/clipper/cctbx/clipper_cctbx.cpp"]+clipper_contrib_files)

diff --git a/sci-libs/cctbx/files/2013.02.27.0005/0101-system-libccp4.patch b/sci-libs/cctbx/files/2013.02.27.0005/0101-system-libccp4.patch
new file mode 100644
index 0000000..16d088d
--- /dev/null
+++ b/sci-libs/cctbx/files/2013.02.27.0005/0101-system-libccp4.patch
@@ -0,0 +1,15 @@
+ cctbx_sources/iotbx/mtz/object.cpp | 4 ++--
+ 1 file changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/cctbx_sources/iotbx/mtz/object.cpp b/cctbx_sources/iotbx/mtz/object.cpp
+index c6ce383..1975a44 100644
+--- a/cctbx_sources/iotbx/mtz/object.cpp
++++ b/cctbx_sources/iotbx/mtz/object.cpp
+@@ -1,5 +1,5 @@
+-#include <cvecmat.h>
+-#include <ccp4_spg.h>
++#include <ccp4/cvecmat.h>
++#include <ccp4/ccp4_spg.h>
+ #include <scitbx/math/utils.h>
+ #include <iotbx/mtz/batch.h>
+ #include <iotbx/mtz/column.h>

diff --git a/sci-libs/cctbx/files/2013.02.27.0005/0102-dontstrip.patch b/sci-libs/cctbx/files/2013.02.27.0005/0102-dontstrip.patch
new file mode 100644
index 0000000..08118f4
--- /dev/null
+++ b/sci-libs/cctbx/files/2013.02.27.0005/0102-dontstrip.patch
@@ -0,0 +1,25 @@
+ cctbx_sources/libtbx/SConscript | 4 ++--
+ 1 file changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/cctbx_sources/libtbx/SConscript b/cctbx_sources/libtbx/SConscript
+index debf569..46ab8d8 100644
+--- a/cctbx_sources/libtbx/SConscript
++++ b/cctbx_sources/libtbx/SConscript
+@@ -471,7 +471,7 @@ libtbx.scons: Warning: compiling with /MDd:
+     elif libtbx.env.build_options.debug_symbols:
+       lkfl = ["-rdynamic"]
+     else:
+-      lkfl = ["-s"]
++      lkfl = []
+     env_etc.shlinkflags = ["-shared"]
+     if (libtbx.env.build_options.mode == "profile"):
+       env_base.Prepend(LINKFLAGS=["-pg"])
+@@ -589,7 +589,7 @@ else:
+       lkfl = ["-rdynamic"]
+ 
+     else:
+-      lkfl = ["-s"]
++      lkfl = []
+     env_etc.shlinkflags = ["-shared"]
+     if (libtbx.env.build_options.mode == "profile"):
+       env_base.Prepend(LINKFLAGS=["-pg"])

diff --git a/sci-libs/cctbx/files/2013.02.27.0005/0103-respect-cflags.patch b/sci-libs/cctbx/files/2013.02.27.0005/0103-respect-cflags.patch
new file mode 100644
index 0000000..60a3c5b
--- /dev/null
+++ b/sci-libs/cctbx/files/2013.02.27.0005/0103-respect-cflags.patch
@@ -0,0 +1,60 @@
+ cctbx_sources/libtbx/SConscript | 17 ++++++-----------
+ 1 file changed, 6 insertions(+), 11 deletions(-)
+
+diff --git a/cctbx_sources/libtbx/SConscript b/cctbx_sources/libtbx/SConscript
+index c273536..a70dae8 100644
+--- a/cctbx_sources/libtbx/SConscript
++++ b/cctbx_sources/libtbx/SConscript
+@@ -120,7 +120,7 @@ def patch_scons_env_for_ad_hoc_debug(env, O123_replacement=["-O0", "-g"]):
+     for f in env[kw]:
+       if   (f in ["-O1", "-O2", "-O3"]):
+         dbg_ccflags.extend(O123_replacement)
+-      elif (f not in ["-ffast-math", "-funroll-loops"]):
++      elif (f not in []):
+         dbg_ccflags.append(f)
+     env.Replace(**{kw: dbg_ccflags})
+ env_etc.patch_scons_env_for_ad_hoc_debug = patch_scons_env_for_ad_hoc_debug
+@@ -453,9 +453,9 @@ libtbx.scons: Warning: compiling with /MDd:
+       warn_options = gcc_common_warn_options() + ["-Werror"]
+     env_etc.ccflags_base.extend(warn_options)
+     if (libtbx.env.build_options.optimization):
+-      opts = ["-DNDEBUG", "-O3", "-ffast-math"]
++      opts = ["-DNDEBUG"]
+       if (env_etc.gcc_version >= 40100 and is_64bit_architecture):
+-        opts.insert(2, "-funroll-loops")
++        opts.insert(2, )
+     else:
+       opts = ["-O0", "-fno-inline"]
+     if (libtbx.env.build_options.mode == "profile"):
+@@ -565,9 +565,7 @@ else:
+       warn_options = gcc_common_warn_options() + ["-Werror"]
+     env_etc.ccflags_base.extend(warn_options)
+     if (libtbx.env.build_options.optimization):
+-      opts = ["-DNDEBUG", "-O3", "-ffast-math"]
+-      if (env_etc.gcc_version >= 40100 and is_64bit_architecture):
+-        opts.insert(2, "-funroll-loops")
++      opts = ["-DNDEBUG"]
+     else:
+       opts = ["-O0", "-fno-inline"]
+     if (libtbx.env.build_options.mode == "profile"):
+@@ -633,10 +631,7 @@ int main() {
+     env_etc.cxxflags_base = []
+     setup_clang_warning(env_etc, libtbx.env.build_options.warning_level)
+     if (libtbx.env.build_options.optimization):
+-      opts = [
+-        "-DNDEBUG",
+-        "-O3",
+-        "-ffast-math"]
++      opts = ["-DNDEBUG"]
+     else:
+       opts = ["-O0", "-fno-inline"]
+     if (libtbx.env.build_options.debug_symbols):
+@@ -782,7 +777,7 @@ int main() {
+       env_etc.cxxflags_base.append("-fcoalesce-templates")
+     env_etc.cxxflags_base.append("-DBOOST_ALL_NO_LIB")
+     if (libtbx.env.build_options.optimization):
+-      opts = ["-DNDEBUG", "-O3", "-ffast-math"]
++      opts = ["-DNDEBUG"]
+       if (cxx == "c++" and env_etc.gcc_version
+             and env_etc.gcc_version == 40000):
+         opts[1] = "-O2" # Apple's optimizer is broken

diff --git a/sci-libs/cctbx/metadata.xml b/sci-libs/cctbx/metadata.xml
new file mode 100644
index 0000000..a259ded
--- /dev/null
+++ b/sci-libs/cctbx/metadata.xml
@@ -0,0 +1,18 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci-chemistry</herd>
+  <maintainer>
+    <email>jlec@g.o</email>
+    <name>Justin Lecher (jlec)</name>
+  </maintainer>
+  <longdescription>
+	The Computational Crystallography Toolbox (cctbx) is being developed
+	as the open source component of the PHENIX system. The goal of
+	the PHENIX project is to advance automation of macromolecular structure
+	determination. PHENIX depends on the cctbx, but not vice versa. This
+	hierarchical approach enforces a clean design as a reusable library.
+	The cctbx is therefore also useful for small-molecule crystallography
+	and even general scientific applications.
+	</longdescription>
+</pkgmetadata>