Thank you Jared. 
I actually use the AutoDock plugin quite often; it lists the energy scores of all poses but if you want to calculate distances you need to do it from PyMol's main panel (and then the same problem is back - the calculation considers only one docking pose..).

Subject: Re: [PyMOL] Applying the DISTANCE command to a docking ensemble
Date: Fri, 2 Aug 2013 16:11:55 +0000

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:  You can run a .pml script with PyMOL commands as well via:

pymol -c my_script.pml

The Autodock plugin and Iterate_state wiki pages may also be helpful if your different poses are each loaded into a separate state.

Hope that helps,

Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
Old Public Health Building, Room 610
341 East 25th Street
New York, NY 10016

On Aug 2, 2013, at 11:31 AM, Amit <> 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,

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