[Chimera-users] how to specify zone near ligand

Elaine Meng meng at cgl.ucsf.edu
Mon Nov 13 10:05:39 PST 2017


Dear Noob  :-)
There are several ways.  You could first select your ligand and then use menu Select… Zone, or you could use commands.  For example, if “ligand” specifies your ligand, you could use command:

select protein & ligand zr<10

…meaning select protein atoms only, using 10-angstrom zone from “ligand" with residue-based cutoff.  If “ligand” does not specify your ligand, you could use residue name(s) or numbers(s) instead, for example residue HEM in chain A:

select protein & :HEM.A zr<10

Specifying atoms in the command line is described in here (click the “zones” link on the left to go to that section):
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html>

Selecting is described here:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html>
… and Select menu here:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/menu.html#menuselect>

“question” is not a useful subject line (almost everything is a question) so I changed it to something more descriptive.

I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Nov 12, 2017, at 12:11 AM, 等儿会儿 <865199546 at qq.com> wrote:
> 
> dear editor:
> i am a noob with using Chimera. Now, i want to find and select all amino acid surrounding my ligand within a particular range(eg. 10Å),how should i do?
> thanks for your help !
> 
> from a user




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