[Chimera-users] Command Line - Slecting Zone Parameters

[Elaine Meng]

On Feb 11, 2009, at 2:54 PM, Thiruvarangan Ramaraj wrote:

> Hi all,
> I am trying to find all the atoms that lie within a certain  
> distance from a selected chains. I am able to do this by going to  
> select -> zone and giving the distance I want and selecting all the  
> atoms that met my criteria. I would like to do this on command  
> line. I am unable to figure it out.
> Any help would be greatly appreciated.
> Thank You
> Thiru Ramaraj

Hi Thiru,
The following command would select all residues with any atom within  
4.5 angstroms of your current selection:

select sel z<4.5

You could use "za" instead of "z" if you want an atom-based cutoff  
instead of whole residues, > instead of < to get the atoms farther  
away, and of course, a different distance.  Also, you don't have to  
use selections.  For example, this would color all atoms within 5  
angstroms of chain A red:

color red :.a za<5

Description of command-line zone specification:
<http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/ 
atom_spec.html#zones>

More examples appear in various tutorials:
<http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/tutorials/ 
attributes.html#part2>
<http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/tutorials/ 
squalene.html#surfaces>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                       http://www.cgl.ucsf.edu/home/meng/index.html