Re: [PyMOL] Python from PyMOL or PyMOL from Python?
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 -- ___ 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
[PyMOL] hiding unreal bonds
Is there a way to hide unreal bonds? I have a ligand with an oxetane I'm aware that pymol will estimate bonds. I tried to use unfuse and remove_picked but because they're not real bonds I can't select them or unfuse them. [image: Displaying Screen Shot 2015-08-14 at 3.32.15 PM.png] -- ___ 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
Re: [PyMOL] hiding unreal bonds
Have you tried unbond? http://www.pymolwiki.org/index.php/Unbond Cheers On Fri, Aug 14, 2015 at 11:38 PM, Andrew Schaub asch...@uci.edu wrote: Is there a way to hide unreal bonds? I have a ligand with an oxetane I'm aware that pymol will estimate bonds. I tried to use unfuse and remove_picked but because they're not real bonds I can't select them or unfuse them. [image: Displaying Screen Shot 2015-08-14 at 3.32.15 PM.png] -- ___ 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 -- João M. Damas PhD Student Protein Modelling Group ITQB-UNL, Oeiras, Portugal Tel:+351-214469613 -- ___ 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
[PyMOL] Python from PyMOL or PyMOL from Python?
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
