Hello, I have a trajectory of a water box and I want to select, show only, save the waters that move in a zone around the COM of the whole system. Any thoughts? Thanks in advance, Yasser
Hi Yasser, If you can figure out commands to do it for a single frame, then you could put the commands into a per-frame script in MD Movie to execute at each frame. It will probably not be that fast, however, if you're saving a file each time. For example, could use "measure center" to measure center of mass of some set of atoms and add a marker at that point. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#center> ....then display only the stuff that you want to save, using a distance zone from that marker model. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#zones> Then in MD Movie add as per-frame script <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#per-frame> For example, a per-frame script something like: ~display measure center @* mark true modelId #5 display #0:hoh & #5 z<6.5 close #5 write relative #0 displayed #0 ~/Desktop/zone<FRAME>.pdb If your waters are named WAT you would use that instead of HOH, of course, and you may want a different distance zone, different filename and location, etc. Also I wasn't sure if you wanted to save all the atoms in the zone or only the waters. The above shows only waters but you could modify to show whichever atoms you want to save. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 3, 2020, at 3:31 AM, Yasser Almeida <yasser.almeida@gmail.com> wrote:
Hello,
I have a trajectory of a water box and I want to select, show only, save the waters that move in a zone around the COM of the whole system. Any thoughts?
Thanks in advance,
Yasser
Great! That works, thanks a lot! Best, Yasser El vie., 3 jul. 2020 a las 18:04, Elaine Meng (<meng@cgl.ucsf.edu>) escribió:
Hi Yasser, If you can figure out commands to do it for a single frame, then you could put the commands into a per-frame script in MD Movie to execute at each frame. It will probably not be that fast, however, if you're saving a file each time.
For example, could use "measure center" to measure center of mass of some set of atoms and add a marker at that point. < http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#center
....then display only the stuff that you want to save, using a distance zone from that marker model. < http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#zones
Then in MD Movie add as per-frame script < http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.h...
< http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#p...
For example, a per-frame script something like:
~display measure center @* mark true modelId #5 display #0:hoh & #5 z<6.5 close #5 write relative #0 displayed #0 ~/Desktop/zone<FRAME>.pdb
If your waters are named WAT you would use that instead of HOH, of course, and you may want a different distance zone, different filename and location, etc. Also I wasn't sure if you wanted to save all the atoms in the zone or only the waters. The above shows only waters but you could modify to show whichever atoms you want to save.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 3, 2020, at 3:31 AM, Yasser Almeida <yasser.almeida@gmail.com> wrote:
Hello,
I have a trajectory of a water box and I want to select, show only, save the waters that move in a zone around the COM of the whole system. Any thoughts?
Thanks in advance,
Yasser
participants (2)
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Elaine Meng -
Yasser Almeida