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
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?
Christian Rummey wrote:
> dear pymol users!
> I use the Kristian Roter's rtools for easy access pdb files.
> however, if I start a pmyol script (.pml, which I just double-click in
> with a command like
> pdb 1kv2
> to get a pdb file loaded, I get an error which is, unfortunately,
> beyond my pymol/python knowledge:
> PyMOL>pdb 1kv2
> Traceback (most recent call last):
> File "C:\Programme\DeLano Scientific\PyMOL\modules\pymol\parser.py",
> line 255, in parse
> File "<string>", line 1
> pdb 1kv2
> SyntaxError: invalid syntax
> pymol launches as usual after that, and I also can use
> rtools commands without problems within it.
UC Berkeley - Berger Lab