display atom by coordinates
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
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
Hi Bala, Here is the series of Python commands that would do what you want:
from chimera import runCommand as rc rc("sel ions") from chimera.selection import currentAtoms for a in currentAtoms(): a.display = -10 <= a.coord().z <= 35 rc("~sel")
--Eric
Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
On Aug 31, 2013, at 9:34 AM, Elaine Meng meng@cgl.ucsf.edu wrote:
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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participants (3)
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Bala subramanian
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Elaine Meng
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Eric Pettersen