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
