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 -- C. Balasubramanian
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.h...> ... 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.h...>
... 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 -
Elaine Meng -
Eric Pettersen