Hi John, Folmer, First, in reply to Folmer's comment, it did cross my mind whether it was necessary to call Pymol from a script, rather than the reverse. But John gave an example with the file to load as command line argument (./examply.py mymolecule.xyz). If the filename is required internally in the script, that is, AFAIK, cumbersome in Pymol. You could of course have a script that only uses global identifiers (all, n. ca, etc) and run
pymol mymolecule.xyz script.py or pymol mymolecule.xyz script.pml That's what I usually do. The approach shouldn't matter that much though. Yet it is a bit puzzling why the response is slower with Pymol called from Python as compared to direct interaction. To be able to try it, we'd need the definition of 'dosomething'. I've tried a script which called cmd.spectrum instead of the 'dosomething', but couldn't say it was much slower than expected. Cheers, Tsjerk On Thu, Feb 17, 2011 at 9:12 AM, Folmer Fredslund <folm...@gmail.com> wrote: > Dear John > > 2011/2/17 John Russo <lamaro...@gmail.com>: >> Hi, >> I'm sorry for making such beginner's questions but searching the manual, >> google >> or the wiki didn't help me. >> > > You're welcome to ask here. > >> I know how to extend pymol by writing python functions (through the >> extend command). >> But is it possible to do the opposite? I want to write a script that >> loads a molecule, does something >> to it and then displays the pymol window or outputs a png file. I want >> to this without having to >> enter commands in the pymol command line, since I need to put these >> operations in a script, >> without interactive control on pymol. >> >> Example. I want to write a script examply.py with which I can do >> >> ./examply.py mymolecule.xyz >> >> And for output I want to get mymolecule.png or the pymol window with all >> the operations >> already done. >> > > I saw Tsjerks comment, ( and now yours since I write too slow) but was > wondering maybe what you need is more simple. > Do require to load PyMOL from a python script? > > If not, then simply put the commands you need into a text file with > the .pml extension and PyMOL will recognize this when you run it. > > An example file (example.pml) > > load mymolecule.xyz > zoom residue 45-60 > png mymolecule.png > > > Then do like this > pymol -c example.pml > > And you get mymolecule.png > > Best regards, > > -- > Folmer Fredslund > > ------------------------------------------------------------------------------ > The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE: > Pinpoint memory and threading errors before they happen. > Find and fix more than 250 security defects in the development cycle. > Locate bottlenecks in serial and parallel code that limit performance. > http://p.sf.net/sfu/intel-dev2devfeb > _______________________________________________ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands ------------------------------------------------------------------------------ The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE: Pinpoint memory and threading errors before they happen. Find and fix more than 250 security defects in the development cycle. Locate bottlenecks in serial and parallel code that limit performance. http://p.sf.net/sfu/intel-dev2devfeb _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
