I vastly prefer calling the python program from pymol You can call any python program using pymol as:
pymol -r program.py — arg1 arg2 arg3 Or, my full preferred method is: pymol -qrck program.py — arg1 arg2 arg3 These make it quieter, stay on the command line, and not read the .pymolrc file Other options at: http://www.pymolwiki.org/index.php/Command_Line_Options <http://www.pymolwiki.org/index.php/Command_Line_Options> Why is this my preferred method? Running python from pymol doesn’t require you to do any of these arcane things like call “finish_launching”, etc. You just write a python script and run it. > On Aug 14, 2015, at 5:27 AM, Dirk Kostrewa <kostr...@genzentrum.lmu.de> wrote: > > Dear PyMOLers, > > I want to modify atomic coordinates in a python program and make > pictures with PyMOL for making a movie. > > In your experience, is it better to call the python program from PyMOL > or to call PyMOL from the python program? > > And could you please give me any good pointer for your preferred method > (other than the simple scripting tutorial)? > > Best regards, > > Dirk. > > -- > > ******************************************************* > Dirk Kostrewa > Gene Center Munich, A5.07 > Department of Biochemistry > Ludwig-Maximilians-Universität München > Feodor-Lynen-Str. 25 > D-81377 Munich > Germany > Phone: +49-89-2180-76845 > Fax: +49-89-2180-76999 > E-mail: kostr...@genzentrum.lmu.de > WWW: www.genzentrum.lmu.de > ******************************************************* > > > ------------------------------------------------------------------------------ > _______________________________________________ > 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
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