I believe Jmol is the default Sage 3D viewer. However, it seems to be
broken from the notebook. A
from the sage prompt works as expected but not so from the notebook.
Here I get that the problem is in locating the JmolApplet class. It
appears that sagenb is coded to look in the data directory under sagenb
for package data, i.e. relative to the python tree in
site-packages/sagenb/data. After opening the notebook the contents of
the directory can be viewed by pointing one's browser to
In particular the notebook seems to look in
site-packages/sagenb/data/jmol for the JmolApplet class data which was
removed with the advent of the sage-on-gentoo package,
sci-chemistry/jmol. Now here I'm able to get Jmol to work from the
notebook if I create either of the symlinks,
site-packages/sagenb/data/jmol -> /var/www/localhost/htdocs/jmol
There should be a better way to do this but I'm unable to find a way to
get the sagenb package to access external data other than through a
symlink. If the first of the above is done then a version bump of jmol
will require a new sage-notebook install! There is also an "appletweb"
directory that's present under sagenb/data/jmol and I was curious as to
whether it's needed? Is it perhaps a carry-over from the older
Sage-provided jmol stuff?