[Chimera-users] Select zone around COM
yasser.almeida at gmail.com
Mon Jul 6 02:56:12 PDT 2020
Great! That works, thanks a lot!
El vie., 3 jul. 2020 a las 18:04, Elaine Meng (<meng at cgl.ucsf.edu>)
> 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.
> ....then display only the stuff that you want to save, using a distance
> zone from that marker model.
> Then in MD Movie add as per-frame script
> For example, a per-frame script something like:
> 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 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 at gmail.com>
> > 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
> > Thanks in advance,
> > Yasser
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