[Chimera-users] internal coordinates (z-matrix) in chimera
Eric Pettersen
pett at cgl.ucsf.edu
Fri Mar 8 10:01:14 PST 2013
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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