[Chimera-users] display atom by coordinates

Elaine Meng meng at cgl.ucsf.edu
Sat Aug 31 09:34:03 PDT 2013


Hi Bala,
I can't think of a way to do it with Chimera commands only, but it could be done with Python - e.g. you could define a per-frame Python script in the MD Movie dialog as described in the "per-frame scripts" section of this page:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html>

... or if you are using scripts only (not graphical interfaces like the MD Movie dialog) you could include the Chimera command "perframe open [location]yourfile.py" which would open and execute the python script yourfile.py at each display frame.  Of course, you could name the python file something else.
<http://www.rbvi.ucsf.edu/home/meng/docs/UsersGuide/midas/perframe.html>

However, someone else would need to help with writing the actual Python (beyond my skill set, sorry).  It is a long holiday weekend here, so it might be a few days before anybody else replies.
Best,
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 Aug 31, 2013, at 9:15 AM, Bala subramanian wrote:

> Friends,
> I am trying to visualize the md movie of a channel protein. In every frame, i want to display only those ions whose Z coord ranges from -10 to 35 (zcoor of the channel) to make the movie. Is there any simple way ?. Precisely displaying atoms with a condition.
> Thanks in advance,
> Bala




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