[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:

... 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.

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.
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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