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_AtomMeas...
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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