[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/molmol/files/, sci-chemistry/molmol/

[David Seifert]

commit:     36b43ceb873e20cc36cf55b6a2e09c3d01306e49
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Mon Oct 16 04:59:29 2017 +0000
Commit:     David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sun Oct 29 23:20:28 2017 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=36b43ceb

sci-chemistry/molmol: Move patches to dist tarball

Package-Manager: Portage-2.3.11, Repoman-2.3.3

 sci-chemistry/molmol/Manifest                      |    1 +
 sci-chemistry/molmol/files/cast.patch              |   21 -
 sci-chemistry/molmol/files/ldflags.patch           |   13 -
 sci-chemistry/molmol/files/libpng15.patch          |   32 -
 sci-chemistry/molmol/files/molmol-2k_p2-fink.patch |  356 ----
 sci-chemistry/molmol/files/opengl.patch            |   96 -
 sci-chemistry/molmol/files/pjf_RH9_molmol2k2.diff  |  103 --
 sci-chemistry/molmol/files/prefix.patch            |   22 -
 sci-chemistry/molmol/files/wild.patch              | 1866 --------------------
 sci-chemistry/molmol/molmol-2k_p2-r2.ebuild        |   15 +-
 sci-chemistry/molmol/molmol-2k_p2-r3.ebuild        |   17 +-
 sci-chemistry/molmol/molmol-2k_p2-r4.ebuild        |   17 +-
 sci-chemistry/molmol/molmol-2k_p2-r5.ebuild        |   17 +-
 13 files changed, 36 insertions(+), 2540 deletions(-)

diff --git a/sci-chemistry/molmol/Manifest b/sci-chemistry/molmol/Manifest
index 3b9280e4b83..aed5ea92035 100644
--- a/sci-chemistry/molmol/Manifest
+++ b/sci-chemistry/molmol/Manifest
@@ -1,2 +1,3 @@
 DIST molmol-2k.2.0-doc.tar.gz 1062297 SHA256 07e1c3fd04ffe7c9e9d91eaefa0bf72e6d0913a981eec3bf0879bfc65537a6be SHA512 131f747a5762859398ebe9b676a07df56c82c8864ecc035ec914f1dea74dafcd67f87993421dfe5899c640470c7e1e1ef03ae262b04a9b360ae329eb19a331fe WHIRLPOOL b74f47149c4dce8199722075fda17c9cbe22263eec57b647ef543b15386d53b267ee85d5a2c44a4fda7e533fd6ccdafb82fbbbd71e671ec4e1fd58e07363677c
 DIST molmol-2k.2.0-src.tar.gz 1088805 SHA256 1104dcb1b2517581c7d6b1695ff2e92f4076ad34afc48dd896eec38e5acf2287 SHA512 6ab01a6fd3d19752634a2cf22919a20e43d195768bd4bdacd5f0bbe016c3058c94915bad4c7fa64dcd86576be39cad0ae112cb62f5e69ffb10041518101e7a9b WHIRLPOOL e258ede83ac4a8fe9b4a9274588ced7e1294415d864c909ed83e3e56d36512e1388e6f77e45da614bc19992a265d32b739c54aace7faa28971c61a01bba27541
+DIST molmol-patches.tbz2 17528 SHA256 5c3b867762e563c91583e3c965c956e4004edc5532e84a33dce244e0140f596c SHA512 bd94baf0a378f40f854f396963edd9b9e4afc5c56462ee6f8b68889290afdb4c5d9b10878aa5619d0a70153453fe6ee8e7540064522c6db0291ae9162bba9287 WHIRLPOOL 6ebe6ee4142e9c10c5960a0defd3d3b4a7841281b42f865e7777d5f28d878202500442e6afa21e3bd64e691d4ed903712baffe5488abd8dcdec99cb616004380

diff --git a/sci-chemistry/molmol/files/cast.patch b/sci-chemistry/molmol/files/cast.patch
deleted file mode 100644
index 16ac411c76e..00000000000
--- a/sci-chemistry/molmol/files/cast.patch
+++ /dev/null
@@ -1,21 +0,0 @@
-diff --git a/src/data/DataDist.c b/src/data/DataDist.c
-index 7f7121f..18eef33 100644
---- a/src/data/DataDist.c
-+++ b/src/data/DataDist.c
-@@ -27,6 +27,7 @@
- 
- #include <stdio.h>
- #include <stdlib.h>
-+#include <stdint.h>
- 
- #include <hashtab.h>
- 
-@@ -89,7 +90,7 @@ hashInter(void *p, unsigned size)
- {
-   TabEntryInter *entryP = p;
- 
--  return ((unsigned) entryP->atom1P + (unsigned) entryP->atom2P) % size;
-+  return ((unsigned)(uintptr_t) entryP->atom1P + (unsigned)(uintptr_t) entryP->atom2P) % size;
- }
- 
- static int

diff --git a/sci-chemistry/molmol/files/ldflags.patch b/sci-chemistry/molmol/files/ldflags.patch
deleted file mode 100644
index ff6e06ef490..00000000000
--- a/sci-chemistry/molmol/files/ldflags.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-diff --git a/src/main/Makefile b/src/main/Makefile
-index 74530fa..102d1b7 100644
---- a/src/main/Makefile
-+++ b/src/main/Makefile
-@@ -22,7 +22,7 @@ SRC = $(OBJ:.o=.c)
- default: $(PROGRAM)
- 
- $(PROGRAM): $(OBJ) $(LIBS) $(SGLIB) $(TOOLSLIB)
--	$(CC) -o $@ $(CFLAGS) $(OBJ) $(LIBS) $(SGLIB) $(TOOLSLIB) $(SYSLIB)
-+	$(CC) $(CFLAGS) ${LDFLAGS} -o $@ $(OBJ) $(LIBS) $(SGLIB) $(TOOLSLIB) $(SYSLIB)
- 
- clean:
- 	rm -f $(OBJ) $(PROGRAM) core *.ps

diff --git a/sci-chemistry/molmol/files/libpng15.patch b/sci-chemistry/molmol/files/libpng15.patch
deleted file mode 100644
index cd27e490660..00000000000
--- a/sci-chemistry/molmol/files/libpng15.patch
+++ /dev/null
@@ -1,32 +0,0 @@
---- src/motogl/MotOGLDump.c
-+++ src/motogl/MotOGLDump.c
-@@ -248,7 +248,7 @@
- pngErrHand(png_structp pngStrucP, char *errMsg)
- {
-   IORaiseError(errMsg);
--  longjmp(pngStrucP->jmpbuf, 1);
-+  longjmp(png_jmpbuf(pngStrucP), 1);
- }
- #endif
- 
-@@ -357,7 +357,7 @@
-       return IO_RES_ERR;
-     }
- 
--    if (setjmp(pngStrucP->jmpbuf)) {
-+    if (setjmp(png_jmpbuf(pngStrucP))) {
-       if (cBuf != NULL)
- 	free(cBuf);
-       if (fBuf != NULL)
-@@ -368,10 +368,7 @@
- 
-     png_init_io(pngStrucP, ImgFileP);
- 
--    pngInfoP->width = imgW;
--    pngInfoP->height = imgH;
--    pngInfoP->bit_depth = 8;
--    pngInfoP->color_type = PNG_COLOR_TYPE_RGB;
-+    png_set_IHDR(pngStrucP, pngInfoP, imgW, imgH, 8, PNG_COLOR_TYPE_RGB, 0, PNG_COMPRESSION_TYPE_DEFAULT, PNG_FILTER_TYPE_DEFAULT);
-     png_write_info(pngStrucP, pngInfoP);
-   }
- #endif

diff --git a/sci-chemistry/molmol/files/molmol-2k_p2-fink.patch b/sci-chemistry/molmol/files/molmol-2k_p2-fink.patch
deleted file mode 100644
index 14cc83b63e9..00000000000
--- a/sci-chemistry/molmol/files/molmol-2k_p2-fink.patch
+++ /dev/null
@@ -1,356 +0,0 @@
- src/calc/CalcRmsd.c    |    8 ++++----
- src/cmdfig/FigUtil.c   |   46 +++++++++++++++++++++++-----------------------
- src/cmdio/ExWriteSec.c |    6 +++---
- src/data/DataDist.c    |    2 +-
- src/data/DataHand.c    |    8 ++++----
- src/expr/ExprScan.c    |    2 +-
- src/iodev/IODev.c      |    2 --
- src/motif/MotifDial.c  |    2 +-
- src/motif/MotifMainW.c |    4 ++--
- src/os/GFile.c         |    2 +-
- src/prim/PrimDraw.c    |    2 +-
- src/prim/RibbonCalc.c  |   12 ++++++------
- src/pudev/PuMainW.c    |    2 +-
- src/tty/TTY.c          |    2 +-
- tools/src/IsoSurface.c |   22 +++++++++++-----------
- 15 files changed, 60 insertions(+), 62 deletions(-)
-
-diff --git a/src/calc/CalcRmsd.c b/src/calc/CalcRmsd.c
-index 0e4629e..ed99e76 100644
---- a/src/calc/CalcRmsd.c
-+++ b/src/calc/CalcRmsd.c
-@@ -1025,10 +1025,10 @@ CalcRmsd(BOOL fitPairs, char *range, char *glob1, char *glob2,
-   }
- 
-   for (propI = 0; propI < 2; propI++) {
--    if (groupNo == 0 || propI == 0 && ! calc1)
-+    if (groupNo == 0 || (propI == 0 && ! calc1))
-       continue;
- 
--    if (groupNo == 0 || propI == 1 && ! calc2)
-+    if (groupNo == 0 || (propI == 1 && ! calc2))
-       continue;
- 
-     Report("\nAverage RMSD, dev., min. and max of ");
-@@ -1052,8 +1052,8 @@ CalcRmsd(BOOL fitPairs, char *range, char *glob1, char *glob2,
-       Report(" ");
- 
-       for (groupI2 = 0; groupI2 < groupNo; groupI2++) {
--	if (groupI1 < groupI2 &&
--	    groupInfoP[groupI1].membNo != groupInfoP[groupI2].membNo ||
-+	if (((groupI1 < groupI2) &&
-+	    (groupInfoP[groupI1].membNo != groupInfoP[groupI2].membNo)) ||
- 	    groupInfoP[groupI1].membNo == 0 ||
- 	    groupInfoP[groupI2].membNo == 0) {
- 	  groupInfoP[groupI2].stat.avg = 0.0f;
-diff --git a/src/cmdfig/FigUtil.c b/src/cmdfig/FigUtil.c
-index 20d403a..b8dc3a6 100644
---- a/src/cmdfig/FigUtil.c
-+++ b/src/cmdfig/FigUtil.c
-@@ -44,29 +44,29 @@ typedef struct {
- } TabEntry;
- 
- static TabEntry GreekTab[] = {
--  "ALPHA",   'a',
--  "BETA",    'b',
--  "CHI",     'c',
--  "DELTA",   'd',
--  "EPSILON", 'e',
--  "PHI" ,    'f',
--  "GAMMA",   'g',
--  "ETA",     'h',
--  "IOTA",    'i',
--  "KAPPA",   'k',
--  "LAMBDA",  'l',
--  "MU",      'm',
--  "NU",      'n',
--  "PI",      'p',
--  "THETA",   'q',
--  "RHO",     'r',
--  "SIGMA",   's',
--  "TAU",     't',
--  "UPSILON", 'u',
--  "OMEGA",   'w',
--  "XI",      'x',
--  "PSI",     'y',
--  "ZETA",    'z'
-+  {"ALPHA",   'a'},
-+  {"BETA",    'b'},
-+  {"CHI",     'c'},
-+  {"DELTA",   'd'},
-+  {"EPSILON", 'e'},
-+  {"PHI" ,    'f'},
-+  {"GAMMA",   'g'},
-+  {"ETA",     'h'},
-+  {"IOTA",    'i'},
-+  {"KAPPA",   'k'},
-+  {"LAMBDA",  'l'},
-+  {"MU",      'm'},
-+  {"NU",      'n'},
-+  {"PI",      'p'},
-+  {"THETA",   'q'},
-+  {"RHO",     'r'},
-+  {"SIGMA",   's'},
-+  {"TAU",     't'},
-+  {"UPSILON", 'u'},
-+  {"OMEGA",   'w'},
-+  {"XI",      'x'},
-+  {"PSI",     'y'},
-+  {"ZETA",    'z'}
- };
- 
- int
-diff --git a/src/cmdio/ExWriteSec.c b/src/cmdio/ExWriteSec.c
-index 7f705d4..8da8336 100644
---- a/src/cmdio/ExWriteSec.c
-+++ b/src/cmdio/ExWriteSec.c
-@@ -250,9 +250,9 @@ writeSecondary(DhResP *resPA, int resNo)
- 
- 	if (neighLStart != NO_RES) {
- 	  if (num != neighLEnd + 1 ||
--	      neighNum != neighREnd + 1 && neighNum != neighREnd - 1 ||
--	      neighREnd > neighRStart && neighNum != neighREnd + 1 ||
--	      neighREnd < neighRStart && neighNum != neighREnd - 1) {
-+	      (neighNum != neighREnd + 1 && neighNum != neighREnd - 1) ||
-+	      (neighREnd > neighRStart && neighNum != neighREnd + 1) ||
-+	      (neighREnd < neighRStart && neighNum != neighREnd - 1)) {
- 	    writeNeigh(neighLStart, neighLEnd, neighRStart, neighREnd);
- 	    neighLStart = NO_RES;
- 	  } else {
-diff --git a/src/data/DataDist.c b/src/data/DataDist.c
-index 18eef33..c683f9e 100644
---- a/src/data/DataDist.c
-+++ b/src/data/DataDist.c
-@@ -117,7 +117,7 @@ fillIntra(TabEntryIntra *entryP, DhAtomP atom1P, DhAtomP atom2P)
-   entryP->atom2I = DhAtomGetNumber(atom2P);
- 
-   if (entryP->res1I > entryP->res2I ||
--      entryP->res1I == entryP->res2I && entryP->atom1I > entryP->atom2I) {
-+      (entryP->res1I == entryP->res2I && entryP->atom1I > entryP->atom2I)) {
-     t = entryP->res1I;
-     entryP->res1I = entryP->res2I;
-     entryP->res2I = t;
-diff --git a/src/data/DataHand.c b/src/data/DataHand.c
-index b20e29c..368aad3 100644
---- a/src/data/DataHand.c
-+++ b/src/data/DataHand.c
-@@ -2043,8 +2043,8 @@ applyBondList(PropRefP refP, LINLIST bondL, int groupNum,
-       groupNum1 = getGroupNum(bondAddP->res1P->molP);
-       groupNum2 = getGroupNum(bondAddP->res2P->molP);
-       if (atom1P->state == AS_VALID && atom2P->state == AS_VALID &&
--	  (groupNum1 == groupNum && groupNum2 == groupNum ||
--	  groupNum < 0 && groupNum1 != groupNum2))
-+	  ((groupNum1 == groupNum && groupNum2 == groupNum) ||
-+	  (groupNum < 0 && groupNum1 != groupNum2)))
- 	applyF(bondP, atom1P, atom2P, clientData);
-     }
-     bondAddP = nextBondAddP;
-@@ -2367,8 +2367,8 @@ callDistApply(PropRefP refP, DhDistP distP, int groupNum,
-     groupNum1 = getGroupNum(distP->res1P->molP);
-     groupNum2 = getGroupNum(distP->res2P->molP);
-     if (atom1P->state == AS_VALID && atom2P->state == AS_VALID &&
--	(groupNum1 == groupNum && groupNum2 == groupNum ||
--	groupNum < 0 && groupNum1 != groupNum2))
-+	((groupNum1 == groupNum && groupNum2 == groupNum) ||
-+	(groupNum < 0 && groupNum1 != groupNum2)))
-       applyF(distP, atom1P, atom2P, clientData);
-   }
- }
-diff --git a/src/expr/ExprScan.c b/src/expr/ExprScan.c
-index dcef69e..6266b4d 100644
---- a/src/expr/ExprScan.c
-+++ b/src/expr/ExprScan.c
-@@ -221,7 +221,7 @@ ExprScanGetSym(void)
- 	for (;;) {
- 	  if (isdigit(ch)) {
- 	    DStrAppChar(StrVal, ch);
--	  } else if (ch == '.' && ExprStr[1] != '.' ||
-+	  } else if ((ch == '.' && ExprStr[1] != '.') ||
- 	      ch == 'e' || ch == 'E') {
- 	    DStrAppChar(StrVal, ch);
- 	    isFloat = TRUE;
-diff --git a/src/iodev/IODev.c b/src/iodev/IODev.c
-index 9c04ce8..aa4f9a7 100644
---- a/src/iodev/IODev.c
-+++ b/src/iodev/IODev.c
-@@ -44,7 +44,6 @@ extern void IOMotifGLDSetDev(void);
- #endif
- #ifdef IO_DEV_MOTIF_OGL
- extern void IOMotifOGLSetDev(void);
--extern void IOMotifOGLDSetDev(void);
- #endif
- #ifdef IO_DEV_MOTIF_XGL
- extern void IOMotifXGLSetDev(void);
-@@ -76,7 +75,6 @@ static DevListEntry DevList[] = {
- #endif
- #ifdef IO_DEV_MOTIF_OGL
-   {"Motif/OpenGL", IOMotifOGLSetDev},
--  {"Motif/OpenGLD", IOMotifOGLDSetDev},
- #endif
- #ifdef IO_DEV_MOTIF_XGL
-   {"Motif/XGL", IOMotifXGLSetDev},
-diff --git a/src/motif/MotifDial.c b/src/motif/MotifDial.c
-index 2514549..6e3bfd7 100644
---- a/src/motif/MotifDial.c
-+++ b/src/motif/MotifDial.c
-@@ -1323,7 +1323,7 @@ PuMotifAddGizmoCB(PuGizmo gizmo, PuGizmoCBType type,
- 
-   switch (type) {
-   case PU_CT_ACTIVATE:
--    if (gType == GIZMO_TEXT_FIELD || GIZMO_TEXT)
-+    if (gType == (GIZMO_TEXT_FIELD | GIZMO_TEXT))
-       XtAddCallback(gizmo, XmNactivateCallback, textActivateCB, infoP);
-     else if (gType == GIZMO_BUTTON)
-       XtAddCallback(gizmo, XmNactivateCallback, gizmoGenCB, infoP);
-diff --git a/src/motif/MotifMainW.c b/src/motif/MotifMainW.c
-index abbb444..77ce8fd 100644
---- a/src/motif/MotifMainW.c
-+++ b/src/motif/MotifMainW.c
-@@ -80,8 +80,8 @@ checkPressOrExpose(Display *dpy, XEvent *eventP, XPointer arg)
- {
-   Window *winP = (Window *) arg;
- 
--  return eventP->type == ButtonPress && eventP->xbutton.window == *winP ||
--      eventP->type == Expose && eventP->xexpose.window == *winP;
-+  return (eventP->type == ButtonPress && eventP->xbutton.window == *winP) ||
-+      (eventP->type == Expose && eventP->xexpose.window == *winP);
- }
- 
- static void
-diff --git a/src/os/GFile.c b/src/os/GFile.c
-index d0d63b6..08d48c7 100644
---- a/src/os/GFile.c
-+++ b/src/os/GFile.c
-@@ -385,7 +385,7 @@ GFileEOF(GFile gf)
- {
-   if (gf->format == GF_FORMAT_MEMORY)
-     return gf->currP == NULL ||
--	gf->currP->nextP == NULL && gf->currPos == gf->currP->len;
-+	(gf->currP->nextP == NULL && gf->currPos == gf->currP->len);
-   else
-     return feof(gf->fp);
- }
-diff --git a/src/prim/PrimDraw.c b/src/prim/PrimDraw.c
-index 32bd593..ba89c57 100644
---- a/src/prim/PrimDraw.c
-+++ b/src/prim/PrimDraw.c
-@@ -461,7 +461,7 @@ drawRibbon(PrimObjP primP)
-   }
- 
-   if (partP->paint == RP_ATOM ||
--      partP->paint == RP_ATOM_SMOOTH && partP->polyNo > 0)
-+      (partP->paint == RP_ATOM_SMOOTH && partP->polyNo > 0))
-     SgSetColor(attrP->colR, attrP->colG, attrP->colB);
- 
-   if (partP->paint == RP_ATOM_SMOOTH)
-diff --git a/src/prim/RibbonCalc.c b/src/prim/RibbonCalc.c
-index 09874cf..0849d03 100644
---- a/src/prim/RibbonCalc.c
-+++ b/src/prim/RibbonCalc.c
-@@ -907,7 +907,7 @@ calcStrips(PrimObjP primP, PrimObjP prevP)
-     getSplinePoints(partP, ribbonP, ePar, partP->endPar, ePNo + 1,
- 	parA + sPNo + mPNo - 1, xA + sPNo + mPNo - 1, dzA + sPNo + mPNo - 1);
- 
--  if (partP->style == RS_ROUND && partP->midRad == 0.0f ||
-+  if ((partP->style == RS_ROUND && partP->midRad == 0.0f) ||
-       BreakInterrupted()) {
-     /* draw only one line */
-     partP->traceNo = 1;
-@@ -1128,15 +1128,15 @@ calcStrips(PrimObjP primP, PrimObjP prevP)
- 	Vec3Copy(partP->traceA[traceI].nvA[pointI], nv);
-       }
- 
--      if (pointI == 0 && partP->startStyle == RE_SHARP ||
--	  pointI == pointNo - ePNo && partP->endStyle == RE_ARROW)
-+      if ((pointI == 0 && partP->startStyle == RE_SHARP) ||
-+	  (pointI == pointNo - ePNo && partP->endStyle == RE_ARROW))
- 	Vec3Copy(partP->polyA[polyI].xA[traceNo - 1 - traceI], x);
-       else if (pointI == pointNo - 1 && partP->endStyle == RE_SHARP)
- 	Vec3Copy(partP->polyA[polyI].xA[traceI], x);
-     }
- 
--    if (pointI == 0 && partP->startStyle == RE_SHARP ||
--	pointI == pointNo - ePNo && partP->endStyle == RE_ARROW) {
-+    if ((pointI == 0 && partP->startStyle == RE_SHARP) ||
-+	(pointI == pointNo - ePNo && partP->endStyle == RE_ARROW)) {
-       Vec3Copy(x, dy);
-       Vec3Cross(x, dx);
-       Vec3Copy(partP->polyA[polyI].nv, x);
-@@ -1327,7 +1327,7 @@ RibbonCalc(PrimObjP primP)
- 
-   if (! partP->pointValid || prec != partP->prec ||
-       startRad != partP->startRad ||
--      partP->style == RS_ROUND && midRad != partP->midRad ||
-+      (partP->style == RS_ROUND && midRad != partP->midRad) ||
-       endRad != partP->endRad || radChanged) {
-     for (i = 0; i < partP->traceNo; i++) {
-       free(partP->traceA[i].xA);
-diff --git a/src/pudev/PuMainW.c b/src/pudev/PuMainW.c
-index 73d183b..d287345 100644
---- a/src/pudev/PuMainW.c
-+++ b/src/pudev/PuMainW.c
-@@ -57,7 +57,7 @@ PuSetTextField(PuTextFieldChoice fieldChoice, char *text)
-       if (text[0] != LOCK_CHAR)
- 	return;
-       text++;
--      if (text[0] == '\0' || text[0] == ' ' && text[1] == '\0') {
-+      if (text[0] == '\0' || (text[0] == ' ' && text[1] == '\0')) {
- 	StatusLocked = FALSE;
- 	text = " ";
-       }
-diff --git a/src/tty/TTY.c b/src/tty/TTY.c
-index 0090f75..22adfef 100644
---- a/src/tty/TTY.c
-+++ b/src/tty/TTY.c
-@@ -164,7 +164,7 @@ PuTTYSwitchFullscreen(BOOL onOff)
- void
- PuTTYSetTextField(PuTextFieldChoice fieldChoice, char *text)
- {
--  if (text[0] == '\0' || text[0] == ' ' && text[1] == '\0')
-+  if (text[0] == '\0' || (text[0] == ' ' && text[1] == '\0'))
-     return;
- 
-   switch (fieldChoice) {
-diff --git a/tools/src/IsoSurface.c b/tools/src/IsoSurface.c
-index 5e11a98..09f89d0 100644
---- a/tools/src/IsoSurface.c
-+++ b/tools/src/IsoSurface.c
-@@ -104,19 +104,19 @@ typedef struct {
- } Strip;
- 
- static CubeDesc CubeEven = {
--  0, 3, 5, 6, {{D_0, 1}, {D_0,  2}, {D_0,  3}, {D_0,  4}},
--  3, 0, 5, 1, {{D_0, 0}, {D_MZ, 4}, {D_MY, 1}, {D_PX, 2}},
--  0, 3, 6, 2, {{D_0, 0}, {D_MZ, 3}, {D_PY, 2}, {D_MX, 1}},
--  3, 5, 6, 7, {{D_0, 0}, {D_PX, 3}, {D_PZ, 1}, {D_PY, 4}},
--  5, 0, 6, 4, {{D_0, 0}, {D_MY, 3}, {D_MX, 4}, {D_PZ, 2}}
-+  {{0, 3, 5, 6, {{D_0, 1}, {D_0,  2}, {D_0,  3}, {D_0,  4}}},
-+  {3, 0, 5, 1, {{D_0, 0}, {D_MZ, 4}, {D_MY, 1}, {D_PX, 2}}},
-+  {0, 3, 6, 2, {{D_0, 0}, {D_MZ, 3}, {D_PY, 2}, {D_MX, 1}}},
-+  {3, 5, 6, 7, {{D_0, 0}, {D_PX, 3}, {D_PZ, 1}, {D_PY, 4}}},
-+  {5, 0, 6, 4, {{D_0, 0}, {D_MY, 3}, {D_MX, 4}, {D_PZ, 2}}}}
- };
- 
- static CubeDesc CubeOdd = {
--  1, 2, 7, 4, {{D_0, 1}, {D_0,  2}, {D_0,  3}, {D_0,  4}},
--  2, 1, 7, 3, {{D_0, 0}, {D_MZ, 3}, {D_PX, 2}, {D_PY, 1}},
--  1, 2, 4, 0, {{D_0, 0}, {D_MZ, 4}, {D_MX, 1}, {D_MY, 2}},
--  2, 7, 4, 6, {{D_0, 0}, {D_PY, 4}, {D_PZ, 2}, {D_MX, 3}},
--  7, 1, 4, 5, {{D_0, 0}, {D_PX, 4}, {D_MY, 3}, {D_PZ, 1}}
-+  {{1, 2, 7, 4, {{D_0, 1}, {D_0,  2}, {D_0,  3}, {D_0,  4}}},
-+  {2, 1, 7, 3, {{D_0, 0}, {D_MZ, 3}, {D_PX, 2}, {D_PY, 1}}},
-+  {1, 2, 4, 0, {{D_0, 0}, {D_MZ, 4}, {D_MX, 1}, {D_MY, 2}}},
-+  {2, 7, 4, 6, {{D_0, 0}, {D_PY, 4}, {D_PZ, 2}, {D_MX, 3}}},
-+  {7, 1, 4, 5, {{D_0, 0}, {D_PX, 4}, {D_MY, 3}, {D_PZ, 1}}}}
- };
- 
- static BOOL Initialized = FALSE;
-@@ -158,7 +158,7 @@ fillFaces(TetDesc *tetP)
- static BOOL
- equalPair(int i00, int i01, int i10, int i11)
- {
--  return i00 == i10 && i01 == i11 || i00 == i11 && i01 == i10;
-+  return (i00 == i10 && i01 == i11) || (i00 == i11 && i01 == i10);
- }
- 
- static int

diff --git a/sci-chemistry/molmol/files/opengl.patch b/sci-chemistry/molmol/files/opengl.patch
deleted file mode 100644
index c1db35d9013..00000000000
--- a/sci-chemistry/molmol/files/opengl.patch
+++ /dev/null
@@ -1,96 +0,0 @@
- molmol | 65 +++++++++--------------------------------------------------------
- 1 file changed, 9 insertions(+), 56 deletions(-)
-
-diff --git a/molmol b/molmol
-index 7863225..b6c75ce 100755
---- a/molmol
-+++ b/molmol
-@@ -11,55 +11,8 @@ ostype=`uname`
- osrel=`uname -r`
- osmaj=`echo $osrel | awk -F. '{print $1}'`
- osmin=`echo $osrel | awk -F. '{print $2}'`
--localdev=
--glxdev=
--
--if [ $ostype = "IRIX" -o $ostype = "IRIX64" ]; then
--  if [ $osmaj -eq 6 -a $osmin -ge 2 -o $osmaj -gt 6 ]; then
--    arch=sgi6
--    localdev=Motif/OpenGL
--    glxdev=Motif/OpenGL
--  elif [ $osmaj -eq 5 -a $osmin -ge 3 -o $osmaj -gt 5 ]; then
--    arch=sgi5
--    localdev=Motif/OpenGL
--    glxdev=Motif/OpenGL
--  else
--    arch=sgi4
--    localdev=Motif/GL
--  fi
--  MONITOR=72HZ; export MONITOR
--elif [ $ostype = "AIX" ]; then
--  arch=aix
--  localdev=Motif/OpenGL
--elif [ $ostype = "HP-UX" ]; then
--  arch=hp
--  localdev=Motif/OpenGL
--  glxdev=Motif/OpenGL
--elif [ $ostype = "OSF1" ]; then
--  arch=dec
--  localdev=Motif/OpenGL
--elif [ $ostype = "Linux" ]; then
--  arch=lnx
--  localdev=Motif/OpenGL
--elif [ $ostype = "SunOS" ]; then
--  if [ $osmaj -eq 5 -a $osmin -ge 4 -o $osmaj -gt 5 ]; then
--    arch=sol
--    localdev=Motif/OpenGL
--  else
--    arch=sun
--  fi
--else
--  arch=unknown
--fi
--
--if [ $ostype = "SunOS" ]; then
--  xdpy=/usr/openwin/bin/xdpyinfo
--elif [ $ostype = "HP-UX" ]; then
--  xdpy=/usr/contrib/bin/X11/xdpyinfo
--else
--  xdpy=/usr/bin/X11/xdpyinfo
--fi
--
-+localdev=Motif/OpenGL
-+glxdev=Motif/OpenGL
- printUsage () {
-   echo "Usage: molmol -ht2as [-o dev] [-r range] [-f macro] files"
-   echo ""
-@@ -121,15 +74,15 @@ done
- 
- magictmp=/tmp/molmol_magic$$
- 
--if [ ! -d $HOME/molmol ]; then
--  mkdir $HOME/molmol
-+if [ ! -d $HOME/.molmol ]; then
-+  mkdir $HOME/.molmol
- fi
--startmacro=$HOME/molmol/options.mac
-+startmacro=$HOME/.molmol/options.mac
- cp /dev/null $startmacro
- 
- if [ -n "$*" ]; then
--  if [ -f $HOME/molmol/dump ]; then
--    mv -f $HOME/molmol/dump $HOME/molmol/dump.old
-+  if [ -f $HOME/.molmol/dump ]; then
-+    mv -f $HOME/.molmol/dump $HOME/.molmol/dump.old
-   fi
-   echo "0	long	0x3b7a12f9	MOLMOL" > $magictmp
-   echo "0	long	0xf9127a3b	MOLMOL" >> $magictmp
-@@ -209,7 +162,7 @@ elif [ -x $xdpy ]; then
- fi
- 
- if [ "$input" = "-" -o -n "$nograph" ]; then
--  $MOLMOLHOME/molmol.$arch $xopt
-+  $MOLMOLHOME/molmol $xopt
- else
--  $MOLMOLHOME/molmol.$arch $xopt < /dev/null
-+  $MOLMOLHOME/molmol $xopt < /dev/null
- fi

diff --git a/sci-chemistry/molmol/files/pjf_RH9_molmol2k2.diff b/sci-chemistry/molmol/files/pjf_RH9_molmol2k2.diff
deleted file mode 100644
index 0ad57d93e10..00000000000
--- a/sci-chemistry/molmol/files/pjf_RH9_molmol2k2.diff
+++ /dev/null
@@ -1,103 +0,0 @@
-Only in molmol_rh9: makedef
-diff -ru molmol_rh9_unpatched/makedef.lnx molmol_rh9/makedef.lnx
---- molmol_rh9_unpatched/makedef.lnx	2003-01-20 16:10:18.000000000 -0500
-+++ molmol_rh9/makedef.lnx	2003-05-06 10:40:08.000000000 -0400
-@@ -1,31 +1,38 @@
- # definitions for Linux
- 
--MISSFUNC = -Dsqrtf=sqrt -Dexpf=exp -Dlogf=log -Dpowf=pow \
--           -Dsinf=sin -Dcosf=cos -Dtanf=tan \
--           -Dasinf=asin -Dacosf=acos -Datanf=atan -Datan2f=atan2 \
--           -Dfabsf=fabs -Dceilf=ceil
--MCPPFLAGS = $(MISSFUNC)
--MCFLAGS = -O2
--
--RANLIB = /bin/true
--WAIT   = /usr/bin/sleep 2
--SHELL  = /bin/sh
--CPP    = /lib/cpp
--CC     = /usr/bin/gcc
-+#TIFFDIR = $(TOP)/tiff-v3.4/libtiff
-+#JPEGDIR = $(TOP)/../libjpeg/jpeg-6a
-+#PNGDIR = $(TOP)/../libpng/libpng-0.89c
-+#ZLIBDIR = $(TOP)/../libpng/zlib-1.0.2
-+
-+IMGDEF  = -DTIFF_SUPPORT -DJPEG_SUPPORT -DPNG_SUPPORT
-+IMGLIB  = -ltiff -ljpeg -lpng -lz
-+IMGINCL = # -I$(TIFFDIR) -I$(JPEGDIR) -I$(PNGDIR) -I$(ZLIBDIR)
-+
-+XINCL   = -I/usr/X11R6/include
-+
-+CC=gcc
-+MCPPFLAGS =
-+MCFLAGS =-pipe -O3 -ffast-math -march=i686 -mcpu=i686
-+
-+RANLIB   = /bin/true
-+WAIT     = sleep 2
-+SHELL    = /bin/sh
-+CPP      = /lib/cpp
- 
--SGDEVDIR = x11 no pov rib vrml1 vrml2 ps fm
--
--SGDEVDEF = -DSG_DEV_X11 -DSG_DEV_NO -DSG_DEV_POV -DSG_DEV_RIB -DSG_DEV_VRML1 -DSG_DEV_VRML2 -DSG_DEV_PS -DSG_DEV_CPS -DSG_DEV_FM3 -DSG_DEV_FM4
-+SGDEVDIR = ogl x11 no pov rib vrml1 vrml2 ps fm
-+SGDEVDEF = -DSG_DEV_OGL -DSG_DEV_X11 -DSG_DEV_NO -DSG_DEV_POV -DSG_DEV_RIB -DSG_DEV_VRML1 -DSG_DEV_VRML2 -DSG_DEV_PS -DSG_DEV_CPS -DSG_DEV_FM3 -DSG_DEV_FM4
- 
- PUDEVDIR = motif tty
- PUDEVDEF = -DPU_DEV_MOTIF -DPU_DEV_TTY
- 
--IODEVDIR = motx11 ttyno
--IODEVDEF = -DIO_DEV_MOTIF_X11 -DIO_DEV_TTY_NO
-+IODEVDIR = motogl motx11 ttyno
-+IODEVDEF = -DIO_DEV_MOTIF_OGL -DIO_DEV_MOTIF_X11 -DIO_DEV_TTY_NO
- 
-+OPENGLDEF = -DOPENGL_SGI_STEREO
- MOTIFDEF = -DFUNCPROTO
- 
--SYSLIB   = -L/usr/X11R6/lib -lXm -lXt -lXpm -lX11 -lm -lc -lieee
-+SYSLIB   = -lGLw -lGLU -lGL -lXm -lXpm -lXt -lXext -lX11 -lm
- 
- TOOLSDIR = $(TOP)/tools
--SGDIR    = $(TOP)/sg
-+SGDIR   = $(TOP)/sg
-diff -ru molmol_rh9_unpatched/src/motogl/MotOGL.c molmol_rh9/src/motogl/MotOGL.c
---- molmol_rh9_unpatched/src/motogl/MotOGL.c	2000-05-29 12:31:51.000000000 -0400
-+++ molmol_rh9/src/motogl/MotOGL.c	2003-05-06 11:51:05.000000000 -0400
-@@ -31,7 +31,7 @@
- #include <Xm/XmStrDefs.h>
- 
- #define BOOL MOTIF_BOOL  /* hack to avoid naming conflict */
--#include <X11/GLw/GLwMDrawA.h>
-+#include <GL/GLwMDrawA.h>
- #undef BOOL
- 
- #include <sg.h>
-diff -ru molmol_rh9_unpatched/src/os/GFile.c molmol_rh9/src/os/GFile.c
---- molmol_rh9_unpatched/src/os/GFile.c	2001-06-17 14:59:17.000000000 -0400
-+++ molmol_rh9/src/os/GFile.c	2003-05-06 12:34:34.000000000 -0400
-@@ -30,6 +30,7 @@
- #include <string.h>
- #include <memory.h>
- #include <ctype.h>
-+#include <errno.h>
- 
- #include <linlist.h>
- 
-@@ -38,7 +39,7 @@
- const INT32 GFMagic = 0x3b7a12f9;
- 
- #ifndef __linux__
--extern char *sys_errlist[];
-+extern char *strerror();
- #endif
- extern int errno;
- 
-@@ -81,7 +82,7 @@
- {
-   if (msg == NULL) {
-     if (NextMsg == NULL)
--      msg = sys_errlist[errno];
-+      msg = strerror(errno);
-     else
-       msg = NextMsg;
-   }

diff --git a/sci-chemistry/molmol/files/prefix.patch b/sci-chemistry/molmol/files/prefix.patch
deleted file mode 100644
index 89f17b2e984..00000000000
--- a/sci-chemistry/molmol/files/prefix.patch
+++ /dev/null
@@ -1,22 +0,0 @@
-diff --git a/molmol b/molmol
-index e774abf..9f10558 100755
---- a/molmol
-+++ b/molmol
-@@ -57,7 +57,7 @@ if [ $ostype = "SunOS" ]; then
- elif [ $ostype = "HP-UX" ]; then
-   xdpy=/usr/contrib/bin/X11/xdpyinfo
- else
--  xdpy=/usr/bin/X11/xdpyinfo
-+  xdpy=@GENTOO_PORTAGE_EPREFIX@/usr/bin/xdpyinfo
- fi
- 
- printUsage () {
-@@ -119,7 +119,7 @@ while [ -n "$*" ]; do
-   esac
- done
- 
--magictmp=/tmp/molmol_magic$$
-+magictmp=@GENTOO_PORTAGE_EPREFIX@/tmp/molmol_magic$$
- 
- if [ ! -d $HOME/molmol ]; then
-   mkdir $HOME/molmol

diff --git a/sci-chemistry/molmol/files/wild.patch b/sci-chemistry/molmol/files/wild.patch
deleted file mode 100644
index 8be9baf9220..00000000000
--- a/sci-chemistry/molmol/files/wild.patch
+++ /dev/null
@@ -1,1866 +0,0 @@
- include/cmd_dial.h        |   1 +
- include/cmd_io.h          |   7 +-
- include/cmd_struc.h       |   1 +
- include/curr_dir.h        |   1 +
- include/data_hand.h       |   6 +
- src/cip/cmd_tab.h         |   3 +
- src/cmddial/ExDialColor.c | 314 +++++++++++++++++++++++++++++++-----------
- src/cmddial/ExDialRes.c   | 340 ++++++++++++++++++++++++++++++++++++++++++++++
- src/cmddial/Makefile      |   2 +-
- src/cmdio/ExPdb.c         |  70 +++++++++-
- src/cmdstruc/ExBuild.c    | 123 +++++++++++++++++
- src/data/DataHand.c       | 114 +++++++++++++++-
- src/iodev/IODev.c         |   2 +
- src/main/MolInit.c        |   5 +-
- src/main/MolMol.c         |   2 +-
- src/motif/MotifDial.c     |  32 ++---
- src/motogl/MotOGLDump.c   |   2 +-
- src/os/CurrDir.c          |  46 ++-----
- src/os/ProgDir.c          |  25 +++-
- src/win/WinDial.c         | 255 +++++++++++++++++-----------------
- src/winogl/WinOGLDump.c   |   7 +-
- 21 files changed, 1073 insertions(+), 285 deletions(-)
-
-diff --git a/include/cmd_dial.h b/include/cmd_dial.h
-index f60e918..47fb8f8 100644
---- a/include/cmd_dial.h
-+++ b/include/cmd_dial.h
-@@ -29,6 +29,7 @@ extern ErrCode ExUserInterface(char *);
- 
- extern ErrCode ExDialColor(char *);
- extern ErrCode ExDialMol(char *);
-+extern ErrCode ExDialRes(char *);
- extern ErrCode ExDialMeasure(char *);
- extern ErrCode ExDialRmsd(char *);
- extern ErrCode ExDialSelect(char *);
-diff --git a/include/cmd_io.h b/include/cmd_io.h
-index 79b173c..9a7b12c 100644
---- a/include/cmd_io.h
-+++ b/include/cmd_io.h
-@@ -30,15 +30,16 @@ extern ErrCode ExReadAng(char *);
- extern ErrCode ExReadDg(char *);
- extern ErrCode ExReadDump(char *);
- extern ErrCode ExReadLib(char *);
--extern ErrCode ExReadPdb(char *);
--extern ErrCode ExReadSeq(char *);
--extern ErrCode ExReadShift(char *);
- extern ErrCode ExReadLimit(char *);
- extern ErrCode ExReadListAng(char *);
- extern ErrCode ExReadListDg(char *);
- extern ErrCode ExReadListPdb(char *);
-+extern ErrCode ExReadOldPdb(char *);
- extern ErrCode ExReadOmap(char *);
-+extern ErrCode ExReadPdb(char *);
- extern ErrCode ExReadPot(char *);
-+extern ErrCode ExReadSeq(char *);
-+extern ErrCode ExReadShift(char *);
- extern ErrCode ExReadSybyl(char *);
- extern ErrCode ExReadXyz(char *);
- extern ErrCode ExWriteAng(char *);
-diff --git a/include/cmd_struc.h b/include/cmd_struc.h
-index e0d729f..f4950b9 100644
---- a/include/cmd_struc.h
-+++ b/include/cmd_struc.h
-@@ -33,6 +33,7 @@ extern ErrCode ExAddDist(char *);
- extern ErrCode ExAddLimit(char *);
- extern ErrCode ExAddPseudo(char *);
- extern ErrCode ExAddRes(char *);
-+extern ErrCode ExMakeMolCyclic(char *);
- extern ErrCode ExChangeRes(char *);
- extern ErrCode ExFirstMol(char *);
- extern ErrCode ExFlipAtom(char *);
-diff --git a/include/curr_dir.h b/include/curr_dir.h
-index c7895c4..04e404d 100644
---- a/include/curr_dir.h
-+++ b/include/curr_dir.h
-@@ -26,6 +26,7 @@
- #ifndef _CURR_DIR_H_
- #define _CURR_DIR_H_
- 
-+extern void CurrDirSet(char *dir);
- extern char *CurrDirGet(void);
- 
- #endif  /* _CURR_DIR_H_ */
-diff --git a/include/data_hand.h b/include/data_hand.h
-index 4462328..74a716a 100644
---- a/include/data_hand.h
-+++ b/include/data_hand.h
-@@ -112,6 +112,7 @@ extern void DhMolMoveFirst(DhMolP);
- extern void DhMolDestroy(DhMolP);
- 
- extern DhResP DhResNew(DhMolP, DhResDefP, DhSeqPos);
-+extern DhResP DhResNewCyclic(DhMolP, DhResDefP, DhSeqPos);
- extern void DhResMutate(DhResP, DhResDefP, DhMutationKind);
- extern void DhResSetNeigh(DhResP, DhNeighChoice, DhResP);
- extern BOOL DhResDestroy(DhResP);
-@@ -287,6 +288,7 @@ extern void DhMolGetTransVect(DhMolP, Vec3);
- extern MolAttrP DhMolGetAttr(DhMolP);
- 
- extern DSTR DhResGetName(DhResP);
-+extern DhAtomP DhResGetAtomA(DhResP);
- extern int DhResGetNumber(DhResP);
- 
- extern DSTR DhAtomGetName(DhAtomP);
-@@ -335,6 +337,10 @@ extern void DhResAnglesChanged(DhResP);
- extern void DhResDockPrev(DhResP);
- extern void DhResDockNext(DhResP);
- extern void DhResCalcAtom(DhResP, DSTR);
-+extern DhResP DhResPrev(DhResP resP);
-+extern DhResP DhResNext(DhResP resP);
-+extern DhResP DhResFirst(DhMolP molP);
-+extern DhResP DhResLast(DhMolP molP);
- 
- /* dump/undump */
- 
-diff --git a/src/cip/cmd_tab.h b/src/cip/cmd_tab.h
-index 0b73f65..cf7bc2a 100644
---- a/src/cip/cmd_tab.h
-+++ b/src/cip/cmd_tab.h
-@@ -108,6 +108,7 @@ static CmdTabEntry BuiltinCmdTab[] = {
-   {"DialColor", ExDialColor, US_NONE},
-   {"DialMeasure", ExDialMeasure, US_NONE},
-   {"DialMol", ExDialMol, US_NONE},
-+  {"DialRes", ExDialRes, US_NONE},
-   {"DialRmsd", ExDialRmsd, US_NONE},
-   {"DialSelect", ExDialSelect, US_NONE},
-   {"DialStyle", ExDialStyle, US_NONE},
-@@ -164,6 +165,7 @@ static CmdTabEntry BuiltinCmdTab[] = {
-   {"ListSelectedDist", ExListSelected, US_NONE},
-   {"ListSelectedMol", ExListSelected, US_NONE},
-   {"ListSelectedRes", ExListSelected, US_NONE},
-+  {"MakeMolCyclic", ExMakeMolCyclic, US_ALL},
-   {"MaterialAtom", ExMaterial, US_ALL},
-   {"MaterialBond", ExMaterial, US_ALL},
-   {"MaterialDist", ExMaterial, US_ALL},
-@@ -213,6 +215,7 @@ static CmdTabEntry BuiltinCmdTab[] = {
-   {"ReadListDg", ExReadListDg, US_ALL},
-   {"ReadListPdb", ExReadListPdb, US_ALL},
-   {"ReadLol", ExReadLimit, US_ALL},
-+  {"ReadOldPdb", ExReadOldPdb, US_ALL},
-   {"ReadOmap", ExReadOmap, US_ALL},
-   {"ReadPdb", ExReadPdb, US_ALL},
-   {"ReadPot", ExReadPot, US_ALL},
-diff --git a/src/cmddial/ExDialColor.c b/src/cmddial/ExDialColor.c
-index f960e1d..e827c4f 100644
---- a/src/cmddial/ExDialColor.c
-+++ b/src/cmddial/ExDialColor.c
-@@ -43,6 +43,9 @@
- #define NAME_LEN 100
- #define NUM_LEN 6
- #define CMD_NO 7
-+#define MAXRGBVALUE 255
-+#define ICOLOR(c) (int)   ((float)c * (float)MAXRGBVALUE)
-+#define FCOLOR(c) (float) ((float)c / (float)MAXRGBVALUE)
- 
- #define EPS ((float) 1.0e-5)
- 
-@@ -56,8 +59,8 @@ typedef struct {
- static ColorDesc *ColorList;
- static int ColorNo = 0;
- static BOOL DialOn = FALSE;
--static PuGizmo DialGizmo = NULL, NameGizmo, RGizmo, GGizmo, BGizmo, ColGizmo;
--static DSTR NameStr = NULL, RStr, GStr, BStr;
-+static PuGizmo DialGizmo = NULL, NameGizmo, RGizmo, GGizmo, BGizmo, ColGizmo, rGizmo, gGizmo, bGizmo;
-+static DSTR NameStr = NULL, RStr, GStr, BStr, rStr, gStr, bStr;
- 
- static char *LabelList[] = {
-   "Back",
-@@ -136,22 +139,50 @@ editCB(PuGizmo g, char *name, void *clientData, void *callData)
-   char *field = clientData;
-   PuTextCBStruc *callP = callData;
- 
--  if (field[0] == 'N')
-+  if (field[0] == 'N') {
-     DStrAssignStr(NameStr, callP->newText);
--  else if (field[0] == 'R')
-+  }
-+  else if (field[0] == 'R') {
-     DStrAssignStr(RStr, callP->newText);
--  else if (field[0] == 'G')
-+  }
-+  else if (field[0] == 'G') {
-     DStrAssignStr(GStr, callP->newText);
--  else
-+  }
-+  else if (field[0] == 'B') {
-     DStrAssignStr(BStr, callP->newText);
-+  }
-+  else if (field[0] == 'r') {
-+    DStrAssignStr(rStr, callP->newText);
-+  }
-+  else if (field[0] == 'g') {
-+    DStrAssignStr(gStr, callP->newText);
-+  }
-+  else if (field[0] == 'b') {
-+    DStrAssignStr(bStr, callP->newText);
-+  }
- }
- 
- static void
- updateFields(int colorI)
- {
-+  char buf[10];
-+  float f;
-+
-   PuSetStr(RGizmo, PU_SC_TEXT, ColorList[colorI].r);
-   PuSetStr(GGizmo, PU_SC_TEXT, ColorList[colorI].g);
-   PuSetStr(BGizmo, PU_SC_TEXT, ColorList[colorI].b);
-+
-+  f = atof(ColorList[colorI].r);
-+  (void) sprintf(buf, "%i", ICOLOR(f));
-+  PuSetStr(rGizmo, PU_SC_TEXT, buf);
-+
-+  f = atof(ColorList[colorI].g);
-+  (void) sprintf(buf, "%i", ICOLOR(f));
-+  PuSetStr(gGizmo, PU_SC_TEXT, buf);
-+
-+  f = atof(ColorList[colorI].b);
-+  (void) sprintf(buf, "%i", ICOLOR(f));
-+  PuSetStr(bGizmo, PU_SC_TEXT, buf);
- }
- 
- static void
-@@ -190,17 +221,96 @@ activateCB(PuGizmo g, char *name, void *clientData, void *callData)
- {
-   char *field = clientData;
-   int i;
-+  float f;
-+  char buf[10];
- 
-   if (field[0] == 'N') {
-     for (i = 0; i < ColorNo; i++)
-       if (strcmp(ColorList[i].name, DStrToStr(NameStr)) == 0) {
--	updateFields(i);
--	break;
-+        updateFields(i);
-+        break;
-       }
-   } else {
-+    if (field[0] == 'R') {
-+      f = atof(DStrToStr(RStr));
-+      if (f>1.0) {
-+        f=1.0;
-+        i=MAXRGBVALUE;
-+        sprintf(buf,"%1.3f", FCOLOR(i));
-+        DStrAssignStr(RStr, buf);
-+        PuSetStr(RGizmo, PU_SC_TEXT, buf);
-+      }
-+      sprintf(buf,"%i", ICOLOR(f));
-+      DStrAssignStr(rStr, buf);
-+      PuSetStr(rGizmo, PU_SC_TEXT, buf);
-+    }
-+    else if (field[0] == 'G') {
-+      f = atof(DStrToStr(GStr));
-+      if (f>1.0) {
-+        f=1.0;
-+        i=MAXRGBVALUE;
-+        sprintf(buf,"%1.3f", FCOLOR(i));
-+        DStrAssignStr(GStr, buf);
-+        PuSetStr(GGizmo, PU_SC_TEXT, buf);
-+      }
-+      sprintf(buf,"%i", ICOLOR(f));
-+      DStrAssignStr(gStr, buf);
-+      PuSetStr(gGizmo, PU_SC_TEXT, buf);
-+    }
-+    else if (field[0] == 'B') {
-+      f = atof(DStrToStr(BStr));
-+      if (f>1.0) {
-+        f=1.0;
-+        i=MAXRGBVALUE;
-+        sprintf(buf,"%1.3f", FCOLOR(i));
-+        DStrAssignStr(BStr, buf);
-+        PuSetStr(BGizmo, PU_SC_TEXT, buf);
-+      }
-+      sprintf(buf,"%i", ICOLOR(f));
-+      DStrAssignStr(bStr, buf);
-+      PuSetStr(bGizmo, PU_SC_TEXT, buf);
-+    }
-+    else if (field[0] == 'r') {
-+      i = atoi(DStrToStr(rStr));
-+      if (i>MAXRGBVALUE) {
-+        f=1.0;
-+        i=MAXRGBVALUE;
-+        sprintf(buf,"%i", ICOLOR(f));
-+        DStrAssignStr(rStr, buf);
-+        PuSetStr(rGizmo, PU_SC_TEXT, buf);
-+      }
-+      sprintf(buf,"%1.3f", FCOLOR(i));
-+      DStrAssignStr(RStr, buf);
-+      PuSetStr(RGizmo, PU_SC_TEXT, buf);
-+    }
-+    else if (field[0] == 'g') {
-+      i = atoi(DStrToStr(gStr));
-+      if (i>MAXRGBVALUE) {
-+        f=1.0;
-+        i=MAXRGBVALUE;
-+        sprintf(buf,"%i", ICOLOR(f));
-+        DStrAssignStr(gStr, buf);
-+        PuSetStr(gGizmo, PU_SC_TEXT, buf);
-+      }
-+      sprintf(buf,"%1.3f", FCOLOR(i));
-+      DStrAssignStr(GStr, buf);
-+      PuSetStr(GGizmo, PU_SC_TEXT, buf);
-+    }
-+    else if (field[0] == 'b') {
-+      i = atoi(DStrToStr(bStr));
-+      if (i>MAXRGBVALUE) {
-+        f=1.0;
-+        i=MAXRGBVALUE;
-+        sprintf(buf,"%i", ICOLOR(f));
-+        DStrAssignStr(bStr, buf);
-+        PuSetStr(bGizmo, PU_SC_TEXT, buf);
-+      }
-+      sprintf(buf,"%1.3f", FCOLOR(i));
-+      DStrAssignStr(BStr, buf);
-+      PuSetStr(BGizmo, PU_SC_TEXT, buf);
-+    }
-     showName();
-   }
--
-   showColor();
- }
- 
-@@ -258,13 +368,20 @@ showAttr(AttrP attrP)
- {
-   char buf[10];
- 
--  (void) sprintf(buf, "%5.3f", attrP->colR);
-+  (void) sprintf(buf, "%1.3f", attrP->colR);
-   PuSetStr(RGizmo, PU_SC_TEXT, buf);
--  (void) sprintf(buf, "%5.3f", attrP->colG);
-+  (void) sprintf(buf, "%1.3f", attrP->colG);
-   PuSetStr(GGizmo, PU_SC_TEXT, buf);
--  (void) sprintf(buf, "%5.3f", attrP->colB);
-+  (void) sprintf(buf, "%1.3f", attrP->colB);
-   PuSetStr(BGizmo, PU_SC_TEXT, buf);
- 
-+  (void) sprintf(buf, "%i", ICOLOR(attrP->colR));
-+  PuSetStr(rGizmo, PU_SC_TEXT, buf);
-+  (void) sprintf(buf, "%i", ICOLOR(attrP->colG));
-+  PuSetStr(gGizmo, PU_SC_TEXT, buf);
-+  (void) sprintf(buf, "%i", ICOLOR(attrP->colB));
-+  PuSetStr(bGizmo, PU_SC_TEXT, buf);
-+
-   showName();
-   showColor();
- }
-@@ -315,107 +432,152 @@ buildDial(void)
-   PuGizmo g;
-   PuConstraints con;
-   int i;
--
--  DialGizmo = PuCreateDialog("Color Dialog", 7, 5);
--  PuSetBool(DialGizmo, PU_BC_PLACE_OUTSIDE, TRUE);
--
--  con.x = 0;
--  con.w = 1;
--  con.h = 1;
--
--  g = PuCreateLabel(DialGizmo, "Name");
--  con.y = 0;
--  PuSetConstraints(g, con);
--  PuSwitchGizmo(g, TRUE);
--
--  g = PuCreateLabel(DialGizmo, "Red");
--  con.y = 1;
--  PuSetConstraints(g, con);
--  PuSwitchGizmo(g, TRUE);
--
--  g = PuCreateLabel(DialGizmo, "Green");
--  con.y = 2;
--  PuSetConstraints(g, con);
--  PuSwitchGizmo(g, TRUE);
--
--  g = PuCreateLabel(DialGizmo, "Blue");
--  con.y = 3;
--  PuSetConstraints(g, con);
--  PuSwitchGizmo(g, TRUE);
--
--  con.x = 1;
--  con.w = 2;
--  con.h = 1;
--
-   NameStr = DStrNew();
-+
-   RStr = DStrNew();
-   GStr = DStrNew();
-   BStr = DStrNew();
-+  rStr = DStrNew();
-+  gStr = DStrNew();
-+  bStr = DStrNew();
-+
-   DStrAssignStr(RStr, "0.0");
-   DStrAssignStr(GStr, "0.0");
-   DStrAssignStr(BStr, "0.0");
-+  DStrAssignStr(rStr, "0");
-+  DStrAssignStr(gStr, "0");
-+  DStrAssignStr(bStr, "0");
- 
-+  DialGizmo = PuCreateDialog("Color Dialog", 3, 20);
-+  PuSetBool(DialGizmo, PU_BC_PLACE_OUTSIDE, TRUE);
-+
-+  con.x = 1;
-+  con.y = 0;
-+  con.w = 2;
-+  con.h = 3;
-+  ColGizmo = PuCreateColorField(DialGizmo, "Color");
-+  PuSetConstraints(ColGizmo, con);
-+  PuSetConstraints(ColGizmo, con);
-+  showColor();
-+  PuSwitchGizmo(ColGizmo, TRUE);
-+
-+  con.x = 0;
-+  con.y = 4;
-+  con.w = 1;
-+  con.h = 1;
-+  g = PuCreateLabel(DialGizmo, "Name");
-+  PuSetConstraints(g, con);
-+  PuSwitchGizmo(g, TRUE);
-+  con.x = 1;
-+  con.w = 2;
-+  con.h = 1;
-   NameGizmo = PuCreateTextField(DialGizmo, "Name", DStrToStr(NameStr));
--  con.y = 0;
-   PuSetConstraints(NameGizmo, con);
--  PuSetInt(NameGizmo, PU_IC_TEXT_WIDTH, 13);
-+  PuSetInt(NameGizmo, PU_IC_TEXT_WIDTH, 10);
-   PuAddGizmoCB(NameGizmo, PU_CT_MODIFY, editCB, "N", NULL);
-   PuAddGizmoCB(NameGizmo, PU_CT_ACTIVATE, activateCB, "N", NULL);
-   showName();
-   PuSwitchGizmo(NameGizmo, TRUE);
- 
--  RGizmo = PuCreateTextField(DialGizmo, "Red", DStrToStr(RStr));
--  con.y = 1;
-+  con.x = 1;
-+  con.y = 5;
-+  con.w = 2;
-+  con.h = 5;
-+  g = PuCreateList(DialGizmo, "Color List");
-+  for (i = 0; i < ColorNo; i++)
-+    PuAddListEntry(g, ColorList[i].name, FALSE);
-+  PuSetConstraints(g, con);
-+  PuSetBool(g, PU_BC_AUTO_DESEL, TRUE);
-+  PuAddGizmoCB(g, PU_CT_SELECT, selectCB, NULL, NULL);
-+  PuSwitchGizmo(g, TRUE);
-+
-+  con.x = 1;
-+  con.y = 11;
-+  con.w = 1;
-+  con.h = 1;
-+  g = PuCreateLabel(DialGizmo, "Float");
-+  PuSetConstraints(g, con);
-+  PuSwitchGizmo(g, TRUE);
-+  con.x = 2;
-+  con.y = 11;
-+  g = PuCreateLabel(DialGizmo, "RGB");
-+  PuSetConstraints(g, con);
-+  PuSwitchGizmo(g, TRUE);
-+
-+  con.x = 0;
-+  con.y = 12;
-+  con.w = 1;
-+  con.h = 1;
-+  g = PuCreateLabel(DialGizmo, "Red");
-+  PuSetConstraints(g, con);
-+  PuSwitchGizmo(g, TRUE);
-+  con.x = 1;
-+  RGizmo = PuCreateTextField(DialGizmo, "RED", DStrToStr(RStr));
-   PuSetConstraints(RGizmo, con);
-   PuSetInt(RGizmo, PU_IC_TEXT_WIDTH, NUM_LEN);
-   PuAddGizmoCB(RGizmo, PU_CT_MODIFY, editCB, "R", NULL);
-   PuAddGizmoCB(RGizmo, PU_CT_ACTIVATE, activateCB, "R", NULL);
-   PuSwitchGizmo(RGizmo, TRUE);
-+  con.x = 2;
-+  rGizmo = PuCreateTextField(DialGizmo, "red", DStrToStr(rStr));
-+  PuSetConstraints(rGizmo, con);
-+  PuSetInt(rGizmo, PU_IC_TEXT_WIDTH, NUM_LEN);
-+  PuAddGizmoCB(rGizmo, PU_CT_MODIFY, editCB, "r", NULL);
-+  PuAddGizmoCB(rGizmo, PU_CT_ACTIVATE, activateCB, "r", NULL);
-+  PuSwitchGizmo(rGizmo, TRUE);
- 
--  GGizmo = PuCreateTextField(DialGizmo, "Green", DStrToStr(GStr));
--  con.y = 2;
-+  con.x = 0;
-+  con.y = 13;
-+  con.w = 1;
-+  con.h = 1;
-+  g = PuCreateLabel(DialGizmo, "Green");
-+  PuSetConstraints(g, con);
-+  PuSwitchGizmo(g, TRUE);
-+  con.x = 1;
-+  GGizmo = PuCreateTextField(DialGizmo, "GREEN", DStrToStr(GStr));
-   PuSetConstraints(GGizmo, con);
-   PuSetInt(GGizmo, PU_IC_TEXT_WIDTH, NUM_LEN);
-   PuAddGizmoCB(GGizmo, PU_CT_MODIFY, editCB, "G", NULL);
-   PuAddGizmoCB(GGizmo, PU_CT_ACTIVATE, activateCB, "G", NULL);
-   PuSwitchGizmo(GGizmo, TRUE);
-+  con.x = 2;
-+  gGizmo = PuCreateTextField(DialGizmo, "green", DStrToStr(gStr));
-+  PuSetConstraints(gGizmo, con);
-+  PuSetInt(gGizmo, PU_IC_TEXT_WIDTH, NUM_LEN);
-+  PuAddGizmoCB(gGizmo, PU_CT_MODIFY, editCB, "g", NULL);
-+  PuAddGizmoCB(gGizmo, PU_CT_ACTIVATE, activateCB, "g", NULL);
-+  PuSwitchGizmo(gGizmo, TRUE);
- 
--  BGizmo = PuCreateTextField(DialGizmo, "Blue", DStrToStr(BStr));
--  con.y = 3;
-+  con.x = 0;
-+  con.y = 14;
-+  con.w = 1;
-+  con.h = 1;
-+  g = PuCreateLabel(DialGizmo, "Blue");
-+  PuSetConstraints(g, con);
-+  PuSwitchGizmo(g, TRUE);
-+  con.x = 1;
-+  BGizmo = PuCreateTextField(DialGizmo, "BLUE", DStrToStr(BStr));
-   PuSetConstraints(BGizmo, con);
-   PuSetInt(BGizmo, PU_IC_TEXT_WIDTH, NUM_LEN);
-   PuAddGizmoCB(BGizmo, PU_CT_MODIFY, editCB, "B", NULL);
-   PuAddGizmoCB(BGizmo, PU_CT_ACTIVATE, activateCB, "B", NULL);
-   PuSwitchGizmo(BGizmo, TRUE);
-+  con.x = 2;
-+  bGizmo = PuCreateTextField(DialGizmo, "blue", DStrToStr(bStr));
-+  PuSetConstraints(bGizmo, con);
-+  PuSetInt(bGizmo, PU_IC_TEXT_WIDTH, NUM_LEN);
-+  PuAddGizmoCB(bGizmo, PU_CT_MODIFY, editCB, "b", NULL);
-+  PuAddGizmoCB(bGizmo, PU_CT_ACTIVATE, activateCB, "b", NULL);
-+  PuSwitchGizmo(bGizmo, TRUE);
- 
--  ColGizmo = PuCreateColorField(DialGizmo, "Color");
--  con.x = 3;
--  con.y = 0;
--  con.w = 2;
--  con.h = 4;
--  PuSetConstraints(ColGizmo, con);
--  showColor();
--  PuSwitchGizmo(ColGizmo, TRUE);
--
--  g = PuCreateList(DialGizmo, "Color List");
--  for (i = 0; i < ColorNo; i++)
--    PuAddListEntry(g, ColorList[i].name, FALSE);
--  con.x = 5;
--  con.y = 0;
--  con.w = 2;
--  con.h = 4;
--  PuSetConstraints(g, con);
--  PuSetBool(g, PU_BC_AUTO_DESEL, TRUE);
--  PuAddGizmoCB(g, PU_CT_SELECT, selectCB, NULL, NULL);
--  PuSwitchGizmo(g, TRUE);
--
--  con.y = 4;
-+  con.x = 0;
-+  con.y = 15;
-   con.w = 1;
-   con.h = 1;
--
-   for (i = 0; i < CMD_NO; i++) {
-     g = PuCreateButton(DialGizmo, LabelList[i]);
--    con.x = i;
-+    con.x = i%3;
-+	if (i%3 == 0) con.y++;
-     PuSetConstraints(g, con);
-     PuAddGizmoCB(g, PU_CT_ACTIVATE, cmdCB, NULL, NULL);
-     PuSwitchGizmo(g, TRUE);
-diff --git a/src/cmddial/ExDialRes.c b/src/cmddial/ExDialRes.c
-new file mode 100644
-index 0000000..06925ff
---- /dev/null
-+++ b/src/cmddial/ExDialRes.c
-@@ -0,0 +1,340 @@
-+/*
-+************************************************************************
-+*
-+*   ExDialMol.c - DialMol command
-+*
-+*   Copyright (c) 1994-98
-+*
-+*   ETH Zuerich
-+*   Institut fuer Molekularbiologie und Biophysik
-+*   ETH-Hoenggerberg
-+*   CH-8093 Zuerich
-+*
-+*   SPECTROSPIN AG
-+*   Industriestr. 26
-+*   CH-8117 Faellanden
-+*
-+*   All Rights Reserved
-+*
-+*   Date of last modification : 98/08/17
-+*   Pathname of SCCS file     : /tmp_mnt/net/sn/homeb/rkoradi/molmol-master/src/cmddial/SCCS/s.ExDialMol.c
-+*   SCCS identification       : 1.10
-+*
-+************************************************************************
-+*/
-+
-+#include <cmd_dial.h>
-+
-+#include <stdio.h>
-+#include <string.h>
-+#include <stdlib.h>
-+
-+#include <break.h>
-+#include <pu.h>
-+#include <arg.h>
-+#include <cip.h>
-+#include <data_hand.h>
-+
-+#define PROP_NO 3
-+
-+typedef struct {
-+  char *label;
-+  char *propName;
-+  char *cmd;
-+} PropDesc;
-+typedef struct {
-+  char *name;
-+  BOOL active;
-+} Residue;
-+
-+static BOOL DialOn = FALSE;
-+static PuGizmo DialGizmo = NULL, ListGizmo;
-+static int CurrProp;
-+static PropRefP CurrRefP;
-+static int MolNo, MolI;
-+static BOOL *MolStateA;
-+static BOOL SuppressUpdate = FALSE;
-+static PropDesc PropTab[] = {
-+  {"sel", PROP_SELECTED, "SelectRes"},
-+  {"disp", PROP_DISPLAYED, "DefPropRes 'displayed'"},
-+  {"move", PROP_MOVABLE, "DefProRes 'movable'"}
-+};
-+static Residue ResidueTab[] = {
-+	{"ARG", FALSE},
-+	{"CYS", FALSE},
-+	{"PRO", FALSE},
-+	{"ASP", FALSE},
-+	{"PHE", FALSE},
-+	{"LEU", FALSE}, 
-+	{"GLU", FALSE},
-+	{"PRO", FALSE},
-+	{"TYR", FALSE},
-+	{"GLY", FALSE},
-+	{"ASN", FALSE},
-+	{"ALA", FALSE},
-+	{"SER", FALSE},
-+	{"THR", FALSE},
-+	{"LYS", FALSE},
-+	{"ILE", FALSE}  
-+};
-+
-+static void
-+countMol(DhResP molP, void *clientData)
-+{
-+  MolNo++;
-+}
-+
-+
-+
-+static void
-+addMol(DhResP molP, void *clientData)
-+{
-+  
-+  
-+  DSTR name;
-+  DSTR residue;
-+  char buf[10];
-+  char buf2[5];
-+  BOOL propVal;
-+  int j;
-+  name = DStrNew();
-+  residue = DStrNew();
-+
-+
-+  j= DhResGetNumber(molP);
-+  (void) sprintf(buf, "%5d " , j);
-+  
-+  DStrAssignStr(name, buf);
-+  DStrAssignStr(residue, buf2);
-+  DStrAppStr(name, " ");
-+  
-+  DStrAppDStr(residue, DhResGetName(molP));
-+  DStrAppDStr(name, DhResGetName(molP));
-+  propVal = DhResGetProp(CurrRefP, molP);
-+  
-+  
-+  
-+  if (! BreakCheck(10)){
-+    PuAddListEntry(ListGizmo, DStrToStr(name), propVal);
-+	
-+  }
-+  
-+  
-+	
-+  MolStateA[MolI] = propVal;
-+
-+  DStrFree(name);
-+  
-+  MolI++;
-+}
-+
-+static void
-+selectMolCB(PuGizmo g, char *name, void *clientData, void *callData)
-+{
-+  PuSelectCBStruc *callP = callData;
-+  DSTR cmd;
-+  BOOL isFirst;
-+  char buf[10];
-+  int num, startI, i;
-+
-+  (void) sscanf(name, "%d", &num);
-+  MolStateA[num - 1] = callP->onOff;
-+
-+  if (! callP->last)
-+    return;
-+
-+  cmd = DStrNew();
-+  DStrAssignStr(cmd, PropTab[CurrProp].cmd);
-+  isFirst = TRUE;
-+
-+  for (i = 0; i < MolNo; i++) {
-+    if (i == 0 || ! MolStateA[i - 1])
-+      startI = i;
-+    if (MolStateA[i] && (i == MolNo - 1 || ! MolStateA[i + 1])) {
-+      if (isFirst)
-+        DStrAppStr(cmd, " 'num = ");
-+      else
-+        DStrAppStr(cmd, ",");
-+      (void) sprintf(buf, "%d", startI + 1);
-+      DStrAppStr(cmd, buf);
-+      if (i > startI) {
-+        DStrAppStr(cmd, "..");
-+        (void) sprintf(buf, "%d", i + 1);
-+        DStrAppStr(cmd, buf);
-+      }
-+
-+      isFirst = FALSE;
-+    }
-+  }
-+
-+  if (isFirst)
-+    DStrAppStr(cmd, " '0'");
-+  else
-+    DStrAppStr(cmd, "'");
-+
-+  SuppressUpdate = TRUE;
-+  CipExecCmd(DStrToStr(cmd));
-+  SuppressUpdate = FALSE;
-+
-+  DStrFree(cmd);
-+}
-+
-+static void
-+buildList(void)
-+{
-+  int lineNo;
-+
-+  MolNo = 0;
-+  DhApplyRes(PropGetRef(PROP_ALL, FALSE), countMol, NULL);
-+  if (MolNo > 0) {
-+    if (MolStateA == NULL)
-+      MolStateA = malloc(MolNo * sizeof(*MolStateA));
-+    else
-+      MolStateA = realloc(MolStateA, MolNo * sizeof(*MolStateA));
-+    lineNo = MolNo;
-+    if (lineNo > 40)
-+      lineNo = 40;
-+  } else {
-+    lineNo = 1;
-+  }
-+
-+  PuSetInt(ListGizmo, PU_IC_ENTRY_NO, lineNo);
-+
-+  MolI = 0;
-+  BreakActivate(TRUE);
-+  DhApplyRes(PropGetRef(PROP_ALL, FALSE), addMol, NULL);
-+  BreakActivate(FALSE);
-+
-+  PuSwitchGizmo(ListGizmo, TRUE);
-+}
-+
-+static void
-+updateList(void)
-+{
-+  if (SuppressUpdate)
-+    return;
-+
-+  PuSwitchGizmo(ListGizmo, FALSE);
-+  PuRemoveListEntries(ListGizmo, 0, MolNo);
-+  buildList();
-+}
-+
-+static void
-+selectPropCB(PuGizmo g, char *name, void *clientData, void *callData)
-+{
-+  PuSelectCBStruc *callP = callData;
-+  PropRefP newPropP;
-+  int i;
-+
-+  if (! callP->onOff)
-+    return;
-+
-+  for (i = 0; i < PROP_NO; i++)
-+    if (strcmp(name, PropTab[i].label) == 0)
-+      break;
-+
-+  newPropP = PropGetRef(PropTab[i].propName, FALSE);
-+
-+  if (newPropP != CurrRefP) {
-+    CurrRefP = newPropP;
-+    CurrProp = i;
-+    updateList();
-+  }
-+}
-+
-+static void
-+popdownCB(PuGizmo g, char *name, void *clientData, void *callData)
-+{
-+  PuSwitchGizmo(DialGizmo, FALSE);
-+  DialOn = FALSE;
-+}
-+
-+static void
-+listCB(void *clientData)
-+{
-+  updateList();
-+}
-+
-+static void
-+helpCB(PuGizmo g, char *name, void *clientData, void *callData)
-+{
-+  CipShowHelpFile(DialGizmo, "DialMol");
-+}
-+
-+static void
-+buildDial(void)
-+{
-+  
-+  PuGizmo g;
-+  int i;
-+
-+  CurrProp = 0;
-+  CurrRefP = PropGetRef(PropTab[CurrProp].propName, FALSE);
-+
-+  DialGizmo = PuCreateDialog("Residue Dialog", 0, 0);
-+  PuSetBool(DialGizmo, PU_BC_PLACE_OUTSIDE, TRUE);
-+
-+  g = PuCreateRadioBox(DialGizmo, "Property");
-+  for (i = 0; i < PROP_NO; i++)
-+    PuAddToggle(g, PropTab[i].label, i == 0);
-+  PuAddGizmoCB(g, PU_CT_SELECT, selectPropCB, NULL, NULL);
-+  PuSwitchGizmo(g, TRUE);
-+
-+  ListGizmo = PuCreateList(DialGizmo, "Molecules");
-+  PuAddGizmoCB(ListGizmo, PU_CT_SELECT, selectMolCB, NULL, NULL);
-+  PuSetBool(ListGizmo, PU_BC_MULT_SEL, TRUE);
-+  buildList();
-+
-+  PuAddGizmoCB(DialGizmo, PU_CT_CLOSE, popdownCB, NULL, NULL);
-+  PuAddGizmoCB(DialGizmo, PU_CT_HELP, helpCB, NULL, NULL);
-+  
-+}
-+
-+ErrCode
-+ExDialRes(char *cmd)
-+{
-+  ArgDescr arg;
-+  EnumEntryDescr enumEntry[2];
-+  ErrCode errCode;
-+
-+  arg.type = AT_ENUM;
-+
-+  ArgInit(&arg, 1);
-+
-+  arg.prompt = "Residue Dialog";
-+  arg.u.enumD.entryP = enumEntry;
-+  arg.u.enumD.n = 2;
-+
-+  enumEntry[0].str = "off";
-+  enumEntry[1].str = "on";
-+
-+  enumEntry[0].onOff = DialOn;
-+  enumEntry[1].onOff = ! DialOn;
-+  if (DialOn)
-+    arg.v.intVal = 0;
-+  else
-+    arg.v.intVal = 1;
-+
-+  errCode = ArgGet(&arg, 1);
-+  if (errCode != EC_OK) {
-+    ArgCleanup(&arg, 1);
-+    return errCode;
-+  }
-+
-+  DialOn = (arg.v.intVal == 1);
-+
-+  ArgCleanup(&arg, 1);
-+
-+  if (DialOn) {
-+    if (DialGizmo == NULL) {
-+      buildDial();
-+      DhAddMolListCB(listCB, NULL);
-+    }
-+    PuSwitchGizmo(DialGizmo, TRUE);
-+  } else {
-+    if (DialGizmo != NULL)
-+      PuSwitchGizmo(DialGizmo, FALSE);
-+  }
-+
-+  return EC_OK;
-+}
-\ No newline at end of file
-diff --git a/src/cmddial/Makefile b/src/cmddial/Makefile
-index d94609d..66fdea9 100644
---- a/src/cmddial/Makefile
-+++ b/src/cmddial/Makefile
-@@ -8,7 +8,7 @@ CPPFLAGS = $(INCLUDES) $(MCPPFLAGS)
- CFLAGS   = $(CPPFLAGS) $(MCFLAGS)
- 
- OBJ = ExDialColor.o ExDialSelect.o ExDialStyle.o ExDialMol.o ExDialMeas.o \
--      ExDialRmsd.o ExUserInterf.o ExRecordMac.o
-+      ExDialRes.o ExDialRmsd.o ExUserInterf.o ExRecordMac.o
- SRC = $(OBJ:.o=.c)
- 
- default: $(LIBDIR)/libcmd.a
-diff --git a/src/cmdio/ExPdb.c b/src/cmdio/ExPdb.c
-index 8447c4c..fde9c73 100644
---- a/src/cmdio/ExPdb.c
-+++ b/src/cmdio/ExPdb.c
-@@ -1,7 +1,7 @@
- /*
- ************************************************************************
- *
--*   ExPdb.c - ReadPdb, ReadListPdb and WritePdb commands
-+*   ExPdb.c - ReadPdb, ReadOldPdb, ReadListPdb and WritePdb commands
- *
- *   Copyright (c) 1994-98
- *
-@@ -105,7 +105,7 @@ compFunc(void *p1, void *p2)
- }
- 
- static void
--readTransTab(BOOL pdbToIntern)
-+readTransTab(BOOL pdbToIntern, BOOL isNewNomenclature)
- {
-   GFile gf;
-   GFileRes res;
-@@ -114,7 +114,7 @@ readTransTab(BOOL pdbToIntern)
- 
-   TransTab = TreeOpen(sizeof(TransTabEntry), compFunc);
-   gf = SetupOpen(PN_PDB_ATOMS, "PdbAtoms", FALSE);
--  if (gf == NULL)
-+  if (gf == NULL || isNewNomenclature)
-     return;
- 
-   if (pdbToIntern) {
-@@ -675,7 +675,7 @@ ExReadPdb(char *cmd)
-     return errCode;
-   }
- 
--  readTransTab(TRUE);
-+  readTransTab(TRUE, TRUE);
-   UnknownErrInit();
- 
-   if (replace) {
-@@ -755,7 +755,7 @@ ExReadListPdb(char *cmd)
- 
-   FileNamePath(fileName);
- 
--  readTransTab(TRUE);
-+  readTransTab(TRUE,TRUE);
-   UnknownErrInit();
-   inName = DStrNew();
-   pdbName = DStrNew();
-@@ -932,7 +932,7 @@ ExWritePdb(char *cmd)
-   if (gf == NULL)
-     return EC_ERROR;
- 
--  readTransTab(FALSE);
-+  readTransTab(FALSE,TRUE);
- 
-   CHECK_RES(GFileWriteStr(gf, "HEADER    Structure from"));
-   CHECK_RES(GFileWriteStr(gf, PROG_NAME));
-@@ -987,3 +987,61 @@ ExWritePdb(char *cmd)
- 
-   return EC_OK;
- }
-+
-+ErrCode
-+ExReadOldPdb(char *cmd)
-+{
-+  BOOL replace;
-+  DSTR name;
-+  int molNo, readNo;
-+  DhMolP *molPA;
-+  ErrCode errCode;
-+  DSTR errStr;
-+
-+  replace = (strncmp(cmd, "Replace", 7) == 0);
-+
-+  name = DStrNew();
-+  errCode = ArgGetFilename(name, CurrDirGet(), "*.pdb", TRUE);
-+  if (errCode != EC_OK) {
-+    DStrFree(name);
-+    return errCode;
-+  }
-+
-+  readTransTab(TRUE, FALSE);
-+  UnknownErrInit();
-+
-+  if (replace) {
-+    molNo = SelMolGet(NULL, 0);
-+    if (molNo > 0) {
-+      molPA = malloc(molNo * sizeof(*molPA));
-+      (void) SelMolGet(molPA, molNo);
-+    }
-+  } else {
-+    molNo = 0;
-+    molPA = NULL;
-+  }
-+
-+  BreakActivate(TRUE);
-+  errCode = readFile(molPA, molNo, name, &readNo);
-+  BreakActivate(FALSE);
-+
-+  DStrFree(name);
-+  TreeClose(TransTab);
-+  if (molNo > 0)
-+    free(molPA);
-+
-+  if (errCode != EC_OK)
-+    return EC_ERROR;
-+
-+  if (replace)
-+    GraphMolChanged(PROP_SELECTED);
-+
-+  errStr = UnknownErrGet();
-+  if (errStr != NULL) {
-+    CipSetError(DStrToStr(errStr));
-+    DStrFree(errStr);
-+    return EC_WARNING;
-+  }
-+
-+  return EC_OK;
-+}
-diff --git a/src/cmdstruc/ExBuild.c b/src/cmdstruc/ExBuild.c
-index 32bc650..7f003b2 100644
---- a/src/cmdstruc/ExBuild.c
-+++ b/src/cmdstruc/ExBuild.c
-@@ -31,11 +31,16 @@
- #include <data_hand.h>
- #include <data_sel.h>
- #include <graph_draw.h>
-+#include <pu.h>
- 
- #define ARG_NUM 1
- 
- static int CurrPos = 1;
- static int CurrKind = 0;
-+static PuTextWindow TextW;
-+static DhMolP LastMolP=NULL;
-+static BOOL messageWindowCreated=FALSE;
-+static BOOL cyclicResidueFound=FALSE;
- 
- ErrCode
- ExNewMol(char *cmd)
-@@ -206,3 +211,121 @@ ExChangeRes(char *cmd)
- 
-   return EC_OK;
- }
-+
-+static void
-+writeInt(int num)
-+{
-+  char buf[10];
-+  (void) sprintf(buf, "%5d ", num);
-+  PuWriteStr(TextW, buf);
-+}
-+
-+static void
-+checkMolCyclic(DhMolP molP, void *clientData)
-+{
-+  DhResP resP;
-+  DSTR resName = DStrNew();
-+  DStrAssignStr(resName, "XXX");
-+
-+  resP = DhResFirst(molP);
-+  while (resP != NULL) {
-+    if (DStrCmp(resName, DhResGetName(resP)) == 0) {
-+      cyclicResidueFound=TRUE;
-+    }
-+    resP = DhResNext(resP);
-+  }
-+
-+  if (cyclicResidueFound && !messageWindowCreated) {
-+    TextW = PuCreateTextWindow("MakeMolCyclic");
-+    PuWriteStr(TextW, "--------------------------------------------------\n");
-+    messageWindowCreated=TRUE;
-+  }
-+  if (cyclicResidueFound) {
-+    PuWriteStr(TextW, "Error -");
-+    writeInt(DhMolGetNumber(molP) + 1);
-+    PuWriteStr(TextW, DStrToStr(DhMolGetName(molP)));
-+    PuWriteStr(TextW, " already made cyclic!\n");
-+  }
-+}
-+
-+static void
-+makeMolCyclic(DhMolP molP, void *clientData)
-+{
-+  DhResP xResP, yResP;
-+  Vec3 firstCoord, lastCoord, midCoord;
-+  DhResP firstResP, lastResP;
-+  DhAtomP caAtomP;
-+  DSTR atomName = DStrNew();
-+  DhResDefP resDefP = (DhResDefP) clientData;
-+
-+  DStrAssignStr(atomName, "CA");
-+
-+  xResP = DhResNewCyclic(molP, resDefP, SP_FIRST);
-+  DhResInit(xResP);
-+  yResP = DhResNewCyclic(molP, resDefP, SP_LAST);
-+  DhResInit(yResP);
-+
-+  xResP = DhResFirst(molP);
-+
-+  firstResP = DhResNext(xResP);
-+  caAtomP = NULL;
-+  while (caAtomP == NULL && firstResP != NULL) {
-+    caAtomP = DhAtomFindName(firstResP, atomName, FALSE);
-+    firstResP = DhResNext(firstResP);
-+  }
-+  if (caAtomP == NULL) {
-+    return;
-+  }
-+  DhAtomGetCoord(caAtomP, firstCoord);
-+
-+  yResP = DhResLast(molP);
-+  lastResP = DhResPrev(yResP);
-+  caAtomP = NULL;
-+  while (caAtomP == NULL && lastResP != NULL) {
-+    caAtomP = DhAtomFindName(lastResP, atomName, FALSE);
-+    lastResP = DhResPrev(lastResP);
-+  }
-+  if (caAtomP == NULL) {
-+    return;
-+  }
-+
-+  DhAtomGetCoord(caAtomP, lastCoord);
-+
-+  midCoord[0] = (firstCoord[0]+lastCoord[0])/2;
-+  midCoord[1] = (firstCoord[1]+lastCoord[1])/2;
-+  midCoord[2] = (firstCoord[2]+lastCoord[2])/2;
-+
-+  DhAtomSetCoord(DhResGetAtomA(xResP), midCoord);
-+  DhAtomSetCoord(DhResGetAtomA(yResP), midCoord);
-+}
-+
-+ErrCode
-+ExMakeMolCyclic(char *cmd)
-+{
-+  int ind=0;
-+  DhResDefP resDefP;
-+  DSTR resName = DStrNew();
-+
-+  messageWindowCreated=FALSE;
-+  cyclicResidueFound=FALSE;
-+  DhApplyMol(PropGetRef(PROP_SELECTED, FALSE), checkMolCyclic, NULL);
-+  if (cyclicResidueFound) {
-+    DSTR msg = DStrNew();
-+    DStrAssignStr(msg, "Error cyclic molecules selected");
-+    PuSetTextField(PU_TF_STATUS, DStrToStr(msg));
-+    DStrFree(msg);
-+    return EC_OK;
-+  }
-+
-+  DStrAssignStr(resName, "XXX");
-+  resDefP = DhResDefGet(resName);
-+  if (resDefP == NULL) {
-+    CipSetError("error cyclic marker residue 'XXX' not found in residue library");
-+    return EC_ERROR;
-+  }
-+
-+  DhApplyMol(PropGetRef(PROP_SELECTED, FALSE), makeMolCyclic, resDefP);
-+  GraphMolChanged(PROP_SELECTED);
-+  GraphRedrawNeeded();
-+  return EC_OK;
-+}
-diff --git a/src/data/DataHand.c b/src/data/DataHand.c
-index 368aad3..d020c20 100644
---- a/src/data/DataHand.c
-+++ b/src/data/DataHand.c
-@@ -994,9 +994,11 @@ BOOL
- DhResDestroy(DhResP resP)
- {
-   /* can only destroy first or last residue of molecule! */
-+  DhMolP molP;
-   if (resP == ListFirst(resP->molP->resL)) {
-+    molP = resP->molP;
-     ListRemove(resP->molP->resL, resP);
--    setEquivI(ListFirst(resP->molP->resL), NULL);
-+    setEquivI((DhResP)ListFirst(molP->resL), NULL);
-     return TRUE;
-   } else if (resP == ListLast(resP->molP->resL)) {
-     ListRemove(resP->molP->resL, resP);
-@@ -2842,6 +2844,18 @@ DhResGetName(DhResP resP)
-   return resP->defP->name;
- }
- 
-+DhAtomP
-+DhResGetAtomA(DhResP resP)
-+{
-+  return resP->atomA;
-+}
-+
-+DhResDefP
-+DhResGetDefP(DhResP resP)
-+{
-+  return resP->defP;
-+}
-+
- int
- DhResGetNumber(DhResP resP)
- {
-@@ -3313,3 +3327,101 @@ DhAltCoordListGet(void)
- {
-   return AltCoordList;
- }
-+
-+static void
-+initResCyclic(DhResP resP)
-+{
-+  DhResDefP defP;
-+  DhResP prevResP, nextResP;
-+  DhAtomP atomP, equivAtomP;
-+  int i;
-+
-+  defP = resP->defP;
-+
-+  resP->neighLeftP = NULL;
-+  resP->neighRightP = NULL;
-+
-+  resP->atomA = malloc(defP->atomNo * sizeof(*resP->atomA));
-+  resP->bondA = malloc(defP->bondNo * sizeof(*resP->bondA));
-+  resP->angleA = malloc(defP->angleNo * sizeof(*resP->angleA));
-+
-+  for (i = 0; i < defP->atomNo; i++)
-+    initAtom(resP->atomA + i, resP);
-+
-+  for (i = defP->firstBondI; i <= defP->lastBondI; i++)
-+    initBond(resP->bondA + i, resP);
-+
-+  for (i = 0; i < defP->angleNo; i++) {
-+    resP->angleA[i].resP = resP;
-+    resP->angleA[i].val = 0.0f;
-+    resP->angleA[i].minVal = DH_ANGLE_MIN;
-+    resP->angleA[i].maxVal = DH_ANGLE_MAX;
-+    resP->angleA[i].changed = FALSE;
-+    resP->angleA[i].propTab = PropNewTab(FALSE);
-+  }
-+
-+  resP->propTab = PropNewTab(FALSE);
-+
-+  for (i = 0; i < EQUIV_NO; i++) {
-+    resP->equivI[i] = -1;
-+  }
-+
-+  prevResP = ListPrev(resP->molP->resL, resP);
-+  nextResP = ListNext(resP->molP->resL, resP);
-+}
-+
-+DhResP
-+DhResNewCyclic(DhMolP molP, DhResDefP defP, DhSeqPos pos)
-+{
-+  struct DhResS resS;
-+  DhResP resP, prevResP, nextResP;
-+
-+  resS.molP = molP;
-+  resS.defP = defP;
-+
-+  if (pos == SP_FIRST) {
-+    nextResP = ListFirst(molP->resL);
-+    if (nextResP == NULL)
-+      resS.num = 1;
-+    else
-+      resS.num = nextResP->num - 1;
-+
-+    resP = ListInsertFirst(molP->resL, &resS);
-+  } else {
-+    prevResP = ListLast(molP->resL);
-+    if (prevResP == NULL)
-+      resS.num = 1;
-+    else
-+      resS.num = prevResP->num + 1;
-+
-+    resP = ListInsertLast(molP->resL, &resS);
-+  }
-+
-+  initResCyclic(resP);
-+
-+  return resP;
-+}
-+
-+DhResP
-+DhResPrev(DhResP resP)
-+{
-+  return (DhResP) ListPrev(resP->molP->resL, resP);
-+}
-+
-+DhResP
-+DhResNext(DhResP resP)
-+{
-+  return (DhResP) ListNext(resP->molP->resL, resP);
-+}
-+
-+DhResP
-+DhResFirst(DhMolP molP)
-+{
-+  return (DhResP) ListFirst(molP->resL);
-+}
-+
-+DhResP
-+DhResLast(DhMolP molP)
-+{
-+  return (DhResP) ListLast(molP->resL);
-+}
-diff --git a/src/iodev/IODev.c b/src/iodev/IODev.c
-index aa4f9a7..9c04ce8 100644
---- a/src/iodev/IODev.c
-+++ b/src/iodev/IODev.c
-@@ -44,6 +44,7 @@ extern void IOMotifGLDSetDev(void);
- #endif
- #ifdef IO_DEV_MOTIF_OGL
- extern void IOMotifOGLSetDev(void);
-+extern void IOMotifOGLDSetDev(void);
- #endif
- #ifdef IO_DEV_MOTIF_XGL
- extern void IOMotifXGLSetDev(void);
-@@ -75,6 +76,7 @@ static DevListEntry DevList[] = {
- #endif
- #ifdef IO_DEV_MOTIF_OGL
-   {"Motif/OpenGL", IOMotifOGLSetDev},
-+  {"Motif/OpenGLD", IOMotifOGLDSetDev},
- #endif
- #ifdef IO_DEV_MOTIF_XGL
-   {"Motif/XGL", IOMotifXGLSetDev},
-diff --git a/src/main/MolInit.c b/src/main/MolInit.c
-index a7c467a..fccccd3 100644
---- a/src/main/MolInit.c
-+++ b/src/main/MolInit.c
-@@ -313,8 +313,9 @@ MolInit(char *defaultDev, int argc, char *argv[], char *macroName)
- 
-   SgSetDoubleBuffer(TRUE);
- 
--  ProgDirSet("MOLMOLHOME", "/usr/molmol");
-+  ProgDirSet("MOLMOLHOME", argv[0]);
-   SetupSetDir("setup");
-+  CurrDirSet(getenv("HOME"));
--  UserFileSetDir(CurrDirGet(), "molmol");
-+  UserFileSetDir(CurrDirGet(), ".molmol");
-   GFileSetErrorHandler(handleFileError);
- 
-@@ -326,7 +327,7 @@ MolInit(char *defaultDev, int argc, char *argv[], char *macroName)
-   IOSetErrorHandler(handleIOError);
- 
-   PuSetTextField(PU_TF_TITLE,
--      "MOLMOL - MOLecule analysis and MOLecule display");
-+      "MOLMOL - MOLecule analysis and MOLecule display - JCU V1.0.8");
- 
-   gf = UserFileOpenRead("par");
-   if (gf != NULL) {
-diff --git a/src/main/MolMol.c b/src/main/MolMol.c
-index 6f825e8..902b50a 100644
---- a/src/main/MolMol.c
-+++ b/src/main/MolMol.c
-@@ -30,5 +30,5 @@
- int
- main(int argc, char *argv[])
- {
--  return MolInit("Motif/X11", argc, argv, NULL);
-+  return MolInit("Motif/OpenGL", argc, argv, NULL);
- }
-diff --git a/src/motif/MotifDial.c b/src/motif/MotifDial.c
-index 6e3bfd7..8fe0c5a 100644
---- a/src/motif/MotifDial.c
-+++ b/src/motif/MotifDial.c
-@@ -1115,26 +1115,24 @@ PuMotifSetStr(PuGizmo gizmo, PuStrChoice choice, char *val)
- void
- PuMotifSetColor(PuGizmo gizmo, float r, float g, float b)
- {
--  Display *dpy;
--  int screen;
--  Pixel pix;
--  XColor col;
-+  Display *display;
-+  Pixel pixel;
-+  XColor color;
-+  Colormap colormap;
- 
--  dpy = XtDisplay(gizmo);
--  screen = DefaultScreen(dpy);
--  XtVaGetValues(gizmo,
--      XmNbackground, &pix,
--      NULL);
-+  display = XtDisplay(gizmo);
-+  XtVaGetValues(gizmo, XmNbackground, &pixel, NULL);
-+  colormap = DefaultColormapOfScreen(XtScreen(gizmo));
- 
--  if (pix == BlackPixel(dpy, screen))
--    return;
-+  color.pixel = pixel;
-+  color.red = FLOAT2SHORT(r);
-+  color.green = FLOAT2SHORT(g);
-+  color.blue = FLOAT2SHORT(b);
-+  color.flags = DoRed | DoGreen | DoBlue;
- 
--  col.pixel = pix;
--  col.red = FLOAT2SHORT(r);
--  col.green = FLOAT2SHORT(g);
--  col.blue = FLOAT2SHORT(b);
--  col.flags = DoRed | DoGreen | DoBlue;
--  XStoreColor(dpy, DefaultColormap(dpy, screen), &col);
-+  XFreeColors(display, colormap, &pixel, 1, 0);
-+  XAllocColor(display, colormap, &color);
-+  XtVaSetValues(gizmo, XmNbackground, color.pixel, NULL);
- }
- 
- void
-diff --git a/src/motogl/MotOGLDump.c b/src/motogl/MotOGLDump.c
-index 54a4222..3bc25cc 100644
---- a/src/motogl/MotOGLDump.c
-+++ b/src/motogl/MotOGLDump.c
-@@ -302,7 +302,7 @@ writeImg(void)
-     TIFFSetField(tif, TIFFTAG_BITSPERSAMPLE, 8);
- 
-     if (Quality < 100)
--      TIFFSetField(tif, TIFFTAG_COMPRESSION, COMPRESSION_PACKBITS);
-+      TIFFSetField(tif, TIFFTAG_COMPRESSION, COMPRESSION_LZW);
-     else
-       TIFFSetField(tif, TIFFTAG_COMPRESSION, COMPRESSION_NONE);
- 
-diff --git a/src/os/CurrDir.c b/src/os/CurrDir.c
-index edee778..7d2b242 100644
---- a/src/os/CurrDir.c
-+++ b/src/os/CurrDir.c
-@@ -26,9 +26,9 @@
- #include <curr_dir.h>
- 
- #include <stdlib.h>
--#ifdef WIN32
--#include <direct.h>
- #include <string.h>
-+#ifdef WIN32
-+#include <direct.h>
- #else
- #include <unistd.h>
- #include <errno.h>
-@@ -36,43 +36,15 @@
- 
- static char *CurrDir = NULL;
- 
-+void
-+CurrDirSet(char *dir)
-+{
-+  CurrDir = malloc(strlen(dir) + 1);
-+  (void) strcpy(CurrDir, dir);
-+}
-+
- char *
- CurrDirGet(void)
- {
--#ifdef WIN32
--  int len, i;
--#else
--  int size = 10;
--#endif
--
--  if (CurrDir != NULL)
--    return CurrDir;
--
--#ifdef WIN32
--  CurrDir = _getcwd(NULL, 0);
--  if (CurrDir != NULL) {
--    len = strlen(CurrDir);
--    for (i = 0; i < len; i++)
--      if (CurrDir[i] == '\\')
--        CurrDir[i] = '/';
--    return CurrDir;
--  }
--#else
--  CurrDir = malloc(size);
--  for (;;) {
--    if (getcwd(CurrDir, size) != NULL)
--      return CurrDir;
--    if (errno != ERANGE)
--      break;
--    size *= 2;
--    CurrDir = realloc(CurrDir, size);
--  }
--#endif
--
--  /* cannot get current directory, return root directory */
--  CurrDir = realloc(CurrDir, 2);
--  CurrDir[0] = '/';
--  CurrDir[1] = '\0';
--
-   return CurrDir;
- }
-diff --git a/src/os/ProgDir.c b/src/os/ProgDir.c
-index 7abb08d..79ede45 100644
---- a/src/os/ProgDir.c
-+++ b/src/os/ProgDir.c
-@@ -45,10 +45,6 @@ ProgDirSet(char *envVar, char *defVal)
-   dir = getenv(envVar);
-   if (dir == NULL) {
-     len = GetModuleFileName(NULL, exePath, sizeof(exePath));
--    if (len == 0) {
--      ProgDir = defVal;
--      return;
--    }
-     len--;
-     while (len > 0 && exePath[len] != '\\')
-       len--;
-@@ -65,9 +61,24 @@ ProgDirSet(char *envVar, char *defVal)
-     if (ProgDir[i] == '\\')
-       ProgDir[i] = '/';
- #else
--  ProgDir = getenv(envVar);
--  if (ProgDir == NULL)
--    ProgDir = defVal;
-+  char *dir;
-+  char *exePath;
-+  int len;
-+  dir = getenv(envVar);
-+  if (dir == NULL) {
-+    exePath = defVal;
-+    len = strlen(exePath);
-+    len--;
-+    while (len > 0 && exePath[len] != '/')
-+      len--;
-+    dir = exePath;
-+  } else {
-+    len = strlen(dir);
-+  }
-+
-+  ProgDir = malloc(len + 1);
-+  (void) strncpy(ProgDir, dir, len);
-+
- #endif
- }
- 
-diff --git a/src/win/WinDial.c b/src/win/WinDial.c
-index 61d6432..e880559 100644
---- a/src/win/WinDial.c
-+++ b/src/win/WinDial.c
-@@ -1072,148 +1072,143 @@ dialProc(HWND w, UINT msgKind, WPARAM wParam, LPARAM lParam)
-       childP = (GizmoInfo *) GetWindowLong(childW, GWL_USERDATA);
- 
-       switch (notifyCode) {
--	case BN_CLICKED:
--	  if (childId < infoP->u.dial.childNo) {
-+        case BN_CLICKED:
-+          if (childId < infoP->u.dial.childNo) {
-             childP = (GizmoInfo *) GetWindowLong(GetFocus(), GWL_USERDATA);
--	    if (childP->type == GIZMO_TOGGLE) {
--	      boxP = childP->u.toggle.boxP;
--	      if (boxP->type == GIZMO_RADIO_BOX) {
--		for (i = 0; i < infoP->u.dial.childNo; i++) {
--		  cP = infoP->u.dial.childPA[i];
--		  if (cP->type != GIZMO_TOGGLE)
--		    continue;
--		  if (cP->u.toggle.boxP != boxP)
--		    continue;
--	          onOff = SendMessage(cP->w, BM_GETCHECK, 0, 0);
--		  if (onOff && cP != childP) {
--		    cP->u.toggle.onOff = FALSE;
--		    SendMessage(cP->w, BM_SETCHECK, FALSE, 0);
--	            selectStruc.onOff = FALSE;
--	            callCB(boxP, PU_CT_SELECT, cP->name, &selectStruc);
--		    break;
--		  }
--		}
--		if (cP != childP) {
--		  childP->u.toggle.onOff = TRUE;
--		  SendMessage(childP->w, BM_SETCHECK, TRUE, 0);
--	          selectStruc.onOff = TRUE;
--	          callCB(boxP, PU_CT_SELECT, childP->name, &selectStruc);
--		}
--	      } else {
--	        onOff = ! SendMessage(childP->w, BM_GETCHECK, 0, 0);
--		childP->u.toggle.onOff = onOff;
--		SendMessage(childP->w, BM_SETCHECK, onOff, 0);
--	        selectStruc.onOff = onOff;
--	        callCB(boxP, PU_CT_SELECT, childP->name, &selectStruc);
--	      }
--	    } else {
--	      callCB(childP, PU_CT_ACTIVATE, childP->name, NULL);
--	      if (childP->type == GIZMO_TEXT_FIELD &&
--		  childP->u.text.historySize > 0)
--		childP->u.text.firstMod = TRUE;
--	    }
--	  } else {
--	    buttonI = childId - infoP->u.dial.childNo;
--	    callCB(infoP, BUTTON_FIRST + buttonI, ButtonLabelA[buttonI], NULL);
--	  }
-+            if (childP->type == GIZMO_TOGGLE) {
-+              boxP = childP->u.toggle.boxP;
-+              if (boxP->type == GIZMO_RADIO_BOX) {
-+                for (i = 0; i < infoP->u.dial.childNo; i++) {
-+                  cP = infoP->u.dial.childPA[i];
-+                  if (cP->type != GIZMO_TOGGLE) continue;
-+                  if (cP->u.toggle.boxP != boxP)  continue;
-+                  onOff = SendMessage(cP->w, BM_GETCHECK, 0, 0);
-+                  if (onOff && cP != childP) {
-+                    cP->u.toggle.onOff = FALSE;
-+                    SendMessage(cP->w, BM_SETCHECK, FALSE, 0);
-+                    selectStruc.onOff = FALSE;
-+                    callCB(boxP, PU_CT_SELECT, cP->name, &selectStruc);
-+                    break;
-+                  }
-+                }
-+                if (cP != childP) {
-+                  childP->u.toggle.onOff = TRUE;
-+                  SendMessage(childP->w, BM_SETCHECK, TRUE, 0);
-+                  selectStruc.onOff = TRUE;
-+                  callCB(boxP, PU_CT_SELECT, childP->name, &selectStruc);
-+                }
-+              } else {
-+                onOff = ! SendMessage(childP->w, BM_GETCHECK, 0, 0);
-+                childP->u.toggle.onOff = onOff;
-+                SendMessage(childP->w, BM_SETCHECK, onOff, 0);
-+                selectStruc.onOff = onOff;
-+                callCB(boxP, PU_CT_SELECT, childP->name, &selectStruc);
-+              }
-+            } else {
-+              callCB(childP, PU_CT_ACTIVATE, childP->name, NULL);
-+              if (childP->type == GIZMO_TEXT_FIELD && childP->u.text.historySize > 0) childP->u.text.firstMod = TRUE;
-+            }
-+          } else {
-+            buttonI = childId - infoP->u.dial.childNo;
-+            callCB(infoP, BUTTON_FIRST + buttonI, ButtonLabelA[buttonI], NULL);
-+          }
-           return TRUE;
--	case EN_UPDATE:
--	  textEdit(childP);
--	  return TRUE;
--	case LBN_SELCHANGE:
--	  for (i = 0; i < childP->u.list.entryNo; i++)
--	    if (SendMessage(childW, LB_GETSEL, i, 0) !=
--	        childP->u.list.entryA[i].onOff)
--	      lastI = i;
- 
--	  for (i = 0; i < childP->u.list.entryNo; i++) {
--	    onOff = SendMessage(childW, LB_GETSEL, i, 0);
--	    if (onOff != childP->u.list.entryA[i].onOff) {
--	      if (! childP->u.list.autoDesel)
-+        case EN_UPDATE:
-+          textEdit(childP);
-+          return TRUE;
-+
-+        case LBN_SELCHANGE:
-+          for (i = 0; i < childP->u.list.entryNo; i++)
-+            if (SendMessage(childW, LB_GETSEL, i, 0) != childP->u.list.entryA[i].onOff)
-+              lastI = i;
-+
-+          for (i = 0; i < childP->u.list.entryNo; i++) {
-+            onOff = SendMessage(childW, LB_GETSEL, i, 0);
-+            if (onOff != childP->u.list.entryA[i].onOff) {
-+              if (! childP->u.list.autoDesel)
-                 childP->u.list.entryA[i].onOff = onOff;
--	      selectStruc.onOff = onOff;
--	      selectStruc.last = (i == lastI);
--	      callCB(childP, PU_CT_SELECT,
--		  childP->u.list.entryA[i].str, &selectStruc);
--	    }
--	  }
--
--	  if (childP->u.list.autoDesel)
--	    SendMessage(childW, LB_SETCURSEL, -1, 0);
--
--	  return TRUE;
-+              selectStruc.onOff = onOff;
-+              selectStruc.last = (i == lastI);
-+              callCB(childP, PU_CT_SELECT,
-+              childP->u.list.entryA[i].str, &selectStruc);
-+            }
-+          }
-+        if (childP->u.list.autoDesel)
-+          SendMessage(childW, LB_SETCURSEL, -1, 0);
-+        return TRUE;
-       }
-+    break;
- 
--      break;
--    case WM_VSCROLL:
--      childW = (HWND) lParam;
--      childP = (GizmoInfo *) GetWindowLong(childW, GWL_USERDATA);
--      scrollCode = LOWORD(wParam);
-+      case WM_VSCROLL:
-+        childW = (HWND) lParam;
-+        childP = (GizmoInfo *) GetWindowLong(childW, GWL_USERDATA);
-+        scrollCode = LOWORD(wParam);
- 
--      if (scrollCode == SB_LINEUP) {
--	upHistory(childP->u.scroll.textP);
--      } else if (scrollCode == SB_LINEDOWN) {
--	downHistory(childP->u.scroll.textP);
--      } else {
--	return FALSE;
--      }
--      return TRUE;
--    case WM_HSCROLL:
--      scrollCode = LOWORD(wParam);
--      if (scrollCode != SB_THUMBPOSITION && scrollCode != SB_THUMBTRACK)
--	return FALSE;
-+        if (scrollCode == SB_LINEUP) {
-+          upHistory(childP->u.scroll.textP);
-+        } else if (scrollCode == SB_LINEDOWN) {
-+          downHistory(childP->u.scroll.textP);
-+        } else {
-+          return FALSE;
-+        }
-+        return TRUE;
-+      case WM_HSCROLL:
-+        scrollCode = LOWORD(wParam);
-+        if (scrollCode != SB_THUMBPOSITION && scrollCode != SB_THUMBTRACK)
-+          return FALSE;
- 
--      scrollPos = (int)(short)HIWORD(wParam);
--      childW = (HWND) lParam;
--      childP = (GizmoInfo *) GetWindowLong(childW, GWL_USERDATA);
-+        scrollPos = (int)(short)HIWORD(wParam);
-+        childW = (HWND) lParam;
-+        childP = (GizmoInfo *) GetWindowLong(childW, GWL_USERDATA);
- 
--      floatStruc.oldVal = childP->u.slider.val;
--      childP->u.slider.val = scrollPos / childP->u.slider.factor;
--      SetScrollPos(childW, SB_CTL,
--	  (int) (childP->u.slider.val * childP->u.slider.factor),
--	  TRUE);
-+        floatStruc.oldVal = childP->u.slider.val;
-+        childP->u.slider.val = scrollPos / childP->u.slider.factor;
-+        SetScrollPos(childW, SB_CTL,
-+        (int) (childP->u.slider.val * childP->u.slider.factor), TRUE);
- 
--      if (childP->u.slider.valuatorCB == NULL) {
--	floatStruc.newVal = childP->u.slider.val;
--	callCB(childP, PU_CT_MODIFY, childP->name, &floatStruc);
--      } else {
--        valStruc.act = PU_MA_ACTIVATE;
--        valStruc.name = childP->name;
--        valStruc.val = childP->u.slider.val;
--        childP->u.slider.valuatorCB(childP, childP->u.slider.clientData, &valStruc);
--      }
-+        if (childP->u.slider.valuatorCB == NULL) {
-+          floatStruc.newVal = childP->u.slider.val;
-+          callCB(childP, PU_CT_MODIFY, childP->name, &floatStruc);
-+        } else {
-+          valStruc.act = PU_MA_ACTIVATE;
-+          valStruc.name = childP->name;
-+          valStruc.val = childP->u.slider.val;
-+          childP->u.slider.valuatorCB(childP, childP->u.slider.clientData, &valStruc);
-+        }
-+        return TRUE;
- 
--      return TRUE;
--    case WM_PAINT:
--      for (childId = 0; childId < infoP->u.dial.childNo; childId++) {
--        childP = infoP->u.dial.childPA[childId];
--	if (childP->type == GIZMO_COLOR_FIELD)
--	  paintColor(childP->w,
--	      childP->u.color.r, childP->u.color.g, childP->u.color.b);
--      }
--      break;
--    case WM_MOVE:
--      if (infoP->u.dial.outside) {
--	WinPlaceChanged(infoP->w);
--	return TRUE;
--      }
--      break;
--    case WM_CLOSE:
--      buttonNo = 0;
--      for (i = 0; i < BUTTON_NO; i++)
--        if (infoP->u.dial.buttonSwitchA[i])
--	  buttonNo++;
--      if (buttonNo == 0)
--	ShowWindow(infoP->w, SW_HIDE);
--      return TRUE;
--    case WM_DESTROY:
--      WinRemoveDialog(w);
--      for (childId = 0; childId < infoP->u.dial.childNo; childId++)
--        freeInfo(infoP->u.dial.childPA[childId]);
--      freeInfo(infoP);
--      return TRUE;
--  }
-+      case WM_PAINT:
-+        for (childId = 0; childId < infoP->u.dial.childNo; childId++) {
-+          childP = infoP->u.dial.childPA[childId];
-+          if (childP->type == GIZMO_COLOR_FIELD)
-+            paintColor(childP->w,
-+            childP->u.color.r, childP->u.color.g, childP->u.color.b);
-+        }
-+        break;
- 
-+      case WM_MOVE:
-+        if (infoP->u.dial.outside) {
-+          WinPlaceChanged(infoP->w);
-+          return TRUE;
-+        }
-+        break;
-+      case WM_CLOSE:
-+        buttonNo = 0;
-+        for (i = 0; i < BUTTON_NO; i++) {
-+          if (infoP->u.dial.buttonSwitchA[i]) buttonNo++;
-+            if (buttonNo == 0) {
-+              ShowWindow(infoP->w, SW_HIDE);
-+          }
-+        }
-+        return TRUE;
-+      case WM_DESTROY:
-+        WinRemoveDialog(w);
-+        for (childId = 0; childId < infoP->u.dial.childNo; childId++)
-+          freeInfo(infoP->u.dial.childPA[childId]);
-+        freeInfo(infoP);
-+        return TRUE;
-+      }
-   return FALSE;
- }
- 
-diff --git a/src/winogl/WinOGLDump.c b/src/winogl/WinOGLDump.c
-index 0a7d61a..a8ce850 100644
---- a/src/winogl/WinOGLDump.c
-+++ b/src/winogl/WinOGLDump.c
-@@ -44,6 +44,7 @@
- #endif
- #ifdef PNG_SUPPORT
- #include <png.h>
-+#include <pngpriv.h>
- #endif
- 
- #include "winogl_int.h"
-@@ -251,7 +252,7 @@ static void
- pngErrHand(png_structp pngStrucP, char *errMsg)
- {
-   IORaiseError(errMsg);
--  longjmp(pngStrucP->jmpbuf, 1);
-+  longjmp(pngStrucP->longjmp_buffer, 1);
- }
- #endif
- 
-@@ -314,7 +315,7 @@ writeImg(void)
-     TIFFSetField(tif, TIFFTAG_BITSPERSAMPLE, 8);
- 
-     if (Quality < 100)
--      TIFFSetField(tif, TIFFTAG_COMPRESSION, COMPRESSION_PACKBITS);
-+      TIFFSetField(tif, TIFFTAG_COMPRESSION, COMPRESSION_LZW);
-     else
-       TIFFSetField(tif, TIFFTAG_COMPRESSION, COMPRESSION_NONE);
- 
-@@ -369,7 +370,7 @@ writeImg(void)
-       return IO_RES_ERR;
-     }
- 
--    if (setjmp(pngStrucP->jmpbuf)) {
-+    if (setjmp(pngStrucP->longjmp_buffer)) {
-       if (cBuf != NULL)
- 	free(cBuf);
-       if (fBuf != NULL)

diff --git a/sci-chemistry/molmol/molmol-2k_p2-r2.ebuild b/sci-chemistry/molmol/molmol-2k_p2-r2.ebuild
index 9fafb28a9e9..888c738d4f1 100644
--- a/sci-chemistry/molmol/molmol-2k_p2-r2.ebuild
+++ b/sci-chemistry/molmol/molmol-2k_p2-r2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2013 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=4
@@ -12,7 +12,8 @@ DESCRIPTION="Publication-quality molecular visualization package"
 HOMEPAGE="http://hugin.ethz.ch/wuthrich/software/molmol/index.html"
 SRC_URI="
 	ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/unix-gzip/${MY_P}-src.tar.gz
-	ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/unix-gzip/${MY_P}-doc.tar.gz"
+	ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/unix-gzip/${MY_P}-doc.tar.gz
+	https://dev.gentoo.org/~soap/distfiles/${PN}-patches.tbz2"
 
 LICENSE="molmol"
 SLOT="0"
@@ -45,12 +46,12 @@ pkg_setup() {
 src_prepare() {
 	rm -rf tiff*
 	# Patch from http://pjf.net/science/molmol.html, where src.rpm is provided
-	epatch "${FILESDIR}"/pjf_RH9_molmol2k2.diff
+	epatch "${WORKDIR}"/patches/pjf_RH9_molmol2k2.diff
 
-	epatch "${FILESDIR}"/prefix.patch
+	epatch "${WORKDIR}"/patches/prefix.patch
 	eprefixify molmol
 
-	epatch "${FILESDIR}"/ldflags.patch
+	epatch "${WORKDIR}"/patches/ldflags.patch
 
 	ln -s makedef.lnx "${S}"/makedef || die
 
@@ -63,8 +64,8 @@ src_prepare() {
 		-e "s:^CC.*:CC = $(tc-getCC):" \
 		-i "${S}"/makedef || die
 
-	epatch "${FILESDIR}"/cast.patch
-	epatch "${FILESDIR}"/libpng15.patch
+	epatch "${WORKDIR}"/patches/cast.patch
+	epatch "${WORKDIR}"/patches/libpng15.patch
 }
 
 src_install() {

diff --git a/sci-chemistry/molmol/molmol-2k_p2-r3.ebuild b/sci-chemistry/molmol/molmol-2k_p2-r3.ebuild
index 318269562f2..22f3e6a03bd 100644
--- a/sci-chemistry/molmol/molmol-2k_p2-r3.ebuild
+++ b/sci-chemistry/molmol/molmol-2k_p2-r3.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2013 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=4
@@ -12,7 +12,8 @@ DESCRIPTION="Publication-quality molecular visualization package"
 HOMEPAGE="http://hugin.ethz.ch/wuthrich/software/molmol/index.html"
 SRC_URI="
 	ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/unix-gzip/${MY_P}-src.tar.gz
-	ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/unix-gzip/${MY_P}-doc.tar.gz"
+	ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/unix-gzip/${MY_P}-doc.tar.gz
+	https://dev.gentoo.org/~soap/distfiles/${PN}-patches.tbz2"
 
 LICENSE="molmol"
 SLOT="0"
@@ -45,12 +46,12 @@ pkg_setup() {
 src_prepare() {
 	rm -rf tiff*
 	# Patch from http://pjf.net/science/molmol.html, where src.rpm is provided
-	epatch "${FILESDIR}"/pjf_RH9_molmol2k2.diff
+	epatch "${WORKDIR}"/patches/pjf_RH9_molmol2k2.diff
 
-	epatch "${FILESDIR}"/prefix.patch
+	epatch "${WORKDIR}"/patches/prefix.patch
 	eprefixify molmol
 
-	epatch "${FILESDIR}"/ldflags.patch
+	epatch "${WORKDIR}"/patches/ldflags.patch
 
 	ln -s makedef.lnx "${S}"/makedef || die
 
@@ -63,12 +64,12 @@ src_prepare() {
 		-e "s:^CC.*:CC = $(tc-getCC):" \
 		-i "${S}"/makedef || die
 
-	epatch "${FILESDIR}"/cast.patch
-	epatch "${FILESDIR}"/libpng15.patch
+	epatch "${WORKDIR}"/patches/cast.patch
+	epatch "${WORKDIR}"/patches/libpng15.patch
 
 	# patch from fink
 	# fixes numerous bad bracings and hopefully the OGL bug 429974
-	epatch "${FILESDIR}"/${P}-fink.patch
+	epatch "${WORKDIR}"/patches/${P}-fink.patch
 }
 
 src_install() {

diff --git a/sci-chemistry/molmol/molmol-2k_p2-r4.ebuild b/sci-chemistry/molmol/molmol-2k_p2-r4.ebuild
index d4034a9d63c..26a29492218 100644
--- a/sci-chemistry/molmol/molmol-2k_p2-r4.ebuild
+++ b/sci-chemistry/molmol/molmol-2k_p2-r4.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=5
@@ -12,7 +12,8 @@ DESCRIPTION="Publication-quality molecular visualization package"
 HOMEPAGE="http://hugin.ethz.ch/wuthrich/software/molmol/index.html"
 SRC_URI="
 	ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/unix-gzip/${MY_P}-src.tar.gz
-	ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/unix-gzip/${MY_P}-doc.tar.gz"
+	ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/unix-gzip/${MY_P}-doc.tar.gz
+	https://dev.gentoo.org/~soap/distfiles/${PN}-patches.tbz2"
 
 LICENSE="molmol"
 SLOT="0"
@@ -45,12 +46,12 @@ pkg_setup() {
 src_prepare() {
 	rm -rf tiff*
 	# Patch from http://pjf.net/science/molmol.html, where src.rpm is provided
-	epatch "${FILESDIR}"/pjf_RH9_molmol2k2.diff
+	epatch "${WORKDIR}"/patches/pjf_RH9_molmol2k2.diff
 
-	epatch "${FILESDIR}"/prefix.patch
+	epatch "${WORKDIR}"/patches/prefix.patch
 	eprefixify molmol
 
-	epatch "${FILESDIR}"/ldflags.patch
+	epatch "${WORKDIR}"/patches/ldflags.patch
 
 	ln -s makedef.lnx "${S}"/makedef || die
 
@@ -63,12 +64,12 @@ src_prepare() {
 		-e "s:^CC.*:CC = $(tc-getCC):" \
 		-i "${S}"/makedef || die
 
-	epatch "${FILESDIR}"/cast.patch
-	epatch "${FILESDIR}"/libpng15.patch
+	epatch "${WORKDIR}"/patches/cast.patch
+	epatch "${WORKDIR}"/patches/libpng15.patch
 
 	# patch from fink
 	# fixes numerous bad bracings and hopefully the OGL bug 429974
-	epatch "${FILESDIR}"/${P}-fink.patch
+	epatch "${WORKDIR}"/patches/${P}-fink.patch
 
 	tc-export AR
 }

diff --git a/sci-chemistry/molmol/molmol-2k_p2-r5.ebuild b/sci-chemistry/molmol/molmol-2k_p2-r5.ebuild
index 16e8b855360..d788caa2005 100644
--- a/sci-chemistry/molmol/molmol-2k_p2-r5.ebuild
+++ b/sci-chemistry/molmol/molmol-2k_p2-r5.ebuild
@@ -12,7 +12,8 @@ DESCRIPTION="Publication-quality molecular visualization package"
 HOMEPAGE="http://hugin.ethz.ch/wuthrich/software/molmol/index.html"
 SRC_URI="
 	ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/unix-gzip/${MY_P}-src.tar.gz
-	ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/unix-gzip/${MY_P}-doc.tar.gz"
+	ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/unix-gzip/${MY_P}-doc.tar.gz
+	https://dev.gentoo.org/~soap/distfiles/${PN}-patches.tbz2"
 
 LICENSE="molmol"
 SLOT="0"
@@ -45,10 +46,10 @@ pkg_setup() {
 src_prepare() {
 	rm -rf tiff*
 	# Patch from http://pjf.net/science/molmol.html, where src.rpm is provided
-	epatch "${FILESDIR}"/pjf_RH9_molmol2k2.diff
+	epatch "${WORKDIR}"/patches/pjf_RH9_molmol2k2.diff
 
-	epatch "${FILESDIR}"/ldflags.patch
-	epatch "${FILESDIR}"/opengl.patch
+	epatch "${WORKDIR}"/patches/ldflags.patch
+	epatch "${WORKDIR}"/patches/opengl.patch
 
 	ln -s makedef.lnx "${S}"/makedef || die
 
@@ -61,14 +62,14 @@ src_prepare() {
 		-e "s:^CC.*:CC = $(tc-getCC):" \
 		-i "${S}"/makedef || die
 
-	epatch "${FILESDIR}"/cast.patch
-	epatch "${FILESDIR}"/libpng15.patch
+	epatch "${WORKDIR}"/patches/cast.patch
+	epatch "${WORKDIR}"/patches/libpng15.patch
 
 	# patch from fink
 	# fixes numerous bad bracings and hopefully the OGL bug 429974
-	epatch "${FILESDIR}"/${P}-fink.patch
+	epatch "${WORKDIR}"/patches/${P}-fink.patch
 
-	epatch "${FILESDIR}"/wild.patch
+	epatch "${WORKDIR}"/patches/wild.patch
 	tc-export AR
 }