Hi Amit -
I'm not sure about working with your AutoDock file, but the way to run PyMOL
without opening the GUI is via "pymol -c" on the command line. For more
command line options, see:
http://www.pymolwiki.org/index.php/Command_Line_Options. You can run a .pml
script with PyMOL commands as well via:
pymol -c my_script.pml
The Autodock plugin<http://www.pymolwiki.org/index.php/Autodock_plugin> and
Iterate_state<http://www.pymolwiki.org/index.php/Iterate_State> wiki pages may
also be helpful if your different poses are each loaded into a separate state.
Hope that helps,
Jared
--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
Old Public Health Building, Room 610
341 East 25th Street
New York, NY 10016
212-263-7898
http://kong.med.nyu.edu/
On Aug 2, 2013, at 11:31 AM, Amit
<[email protected]<mailto:[email protected]>> wrote:
Dear PyMol users,
Does anyone know how to extend the DISTANCE command (for measuring distances
between two atoms) to the entire ensemble in a docking log file? I've been
trying to do so for an AutoDock4 log file (.dlg file) opened by PyMol, but I
only get the distance for the docking pose shown on screen. The other poses are
ignored.
Alternatively, do you know of a python script which does the above without the
need to open PyMol? That would actually be preferable.
Thank you,
Amit.
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