Jacob, I believe rtool will always be usable if you put run <path>/rtools.py into your .pymolrc file.
Andreas > This is an odd concidence, since I was just about to post about > something very similar. > I would like to use rtools commands from a .pml that is read from the > command line (eg - with the -qc flag, instead of using the graphical > interface). > When starting pymol normally, rtools loads and everything is hunky dory. > However, even if I add a "run <path>/rtools.py" command to the .pml > script, none of the rtools commands are recognized. Manually running > rtools.py from within the .pml produces no errors. > Is there a way to use rtools from within a script that never sees the > graphical front end? > > Jacob >