* Jeremy Craven <c.j.cra...@sheffield.ac.uk> [2002-09-26 09:59] wrote:
> 2) Anyhow, (and assuming that I might want to do alignments my own way > anyhow), > I created a script which read in an alignment and created a big long pair_fit > command of the form .... > > pair_fit (tbr and resi 187 and name ca),(bs and resi 170 and name ca), (tbr > and > resi 192 and name ca),(bs and resi 175 and name ca), .... etc > > The script then executed this string with cmd.do > <snip> I'll tackle the second question: > A second little quesion is how do you send command line arguments to a pymol > python script. > > If I say > > PyMOL> run test1.py abcdef > > it says > > Traceback (most recent call last): > File "/usr/lib/python1.5/site-packages/pymol/modules/pymol/parser.py", line > 186, in parse > execfile(args[nest][0],pymol_names,pymol_names) > IOError: [Errno 2] No such file or directory > > whereas test1.py really does exist, and "run test1.py" works fine. > If you write test1.py to be a function definition, e.g.: def make_pair_fit(arg1,arg2,arg3<etc.>): Then "run test1.py" will read the python script to create the definition, but not actually run it. Then you can run it with: make_pair_fit(YourArg1,YourArg2,YourArg3,...) where you've filled in the appropriate values for the arguments. Hope that helps. Cheers, Robert -- Robert L. Campbell, Ph.D. http://biophysics.med.jhmi.edu/rlc r...@k2.med.jhmi.edu phone: 410-614-6313 Research Specialist/X-ray Facility Manager HHMI/Dept. of Biophysics & Biophysical Chem., The Johns Hopkins University PGP Fingerprint: 9B49 3D3F A489 05DC B35C 8E33 F238 A8F5 F635 C0E2
