[Chimera-users] Select zone around COM

[Yasser Almeida]

Great! That works, thanks a lot!

Best,
Yasser

El vie., 3 jul. 2020 a las 18:04, Elaine Meng (<meng at 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.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 at 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
>
>
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