Dear all,

Thank you very much for your help. I am coding it in python and will run in batch mode.
I think it will work.

Chinh

On Sat, Mar 9, 2013 at 2:01 AM, Eric Pettersen <pett@cgl.ucsf.edu> wrote:
Hi Chinh,
If you are able to write a Python script, you could use the info in the Chimera Programmer's Guide

http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide

to write a script to get the values.  There is a programmer's example specifically about atomic-level measurements such as angles and distances:

http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/Main_AtomMeasure.html

Also, Python is reasonably easy to learn, especially if you already know how to program in another language.  There are links to Python tutorials in the Programmer's Guide.

--Eric

                        Eric Pettersen
                        UCSF Computer Graphics Lab
                        http://www.cgl.ucsf.edu

On Mar 8, 2013, at 9:08 AM, Elaine Meng wrote:

Hi Chinh,
For scripting measurements (distance, angle, torsion) you can use commands: distance, angle
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/distance.html>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/angle.html>

These measurements are specified individually.  Chimera does not have an option to write out a Z-matrix, sorry.

More info on writing Chimera scripts to process multiple data files:
<http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Mar 8, 2013, at 12:01 AM, Chinh Su Tran To wrote:

Hi,
I have some results after running docking from DOCK.
I'd like to obtain information of internal coordinates (bond, angle, torsion OR z-matrix).

Could anyone please give me any suggestion how to do that in Chimera? Or if possible, please suggest me some references that can help me find it out.

I have bunch of conformations, so I may not use the gui.
Thank you.
Chinh


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