[Chimera-users] command line zone selection?

Elaine Meng meng at cgl.ucsf.edu
Sat Dec 30 10:08:05 PST 2006

Hi Kenward,
There *is* a command-line way to specify atoms/residues in a zone  
defined by other atoms. It might have been hard to find since it's not  
a separate command, but instead an atom specification that can be used  
with many commands.

The general form is
   command atom-spec za<N
for example
   select ligand za<3.5

to select all atoms within 3.5 angstroms of any ligand atoms.  
Analogously, "za>N" could be used for all atoms farther away than N  
angstroms.  Using "z" or "zr" instead of "za" gives a residue-based  
cutoff - you would always get whole residues even if only parts of them  
fall in the zone. The "command" can be "select" or many other things  
(color, display, etc.).

Here are a couple more examples:
   rlabel ions z<4
(label residues within 4 angstroms of any ions)
   disp #0 & #2 z<5
(display residues in model 0 that are within 5 angstroms of any atoms  
in model 2).

The description in the manual (click the "zones" link):

It can be confusing, so feel free to write back if you have problems  
generating the command needed in your particular situation!
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Dec 30, 2006, at 8:16 AM, Kenward Vaughan wrote:

> I'm putting together a demo for my students this next semester, and  
> was hoping
> to be able to do a zone selection about the ligand. Is this possible  
> with the
> command line?  I haven't been able to pull out a reference for such,  
> yet.
> Certainly I could pull together the list of residues myself, but  
> thought it'd
> be nice to have the command available.  Some students might like to  
> create a
> demo file for their reports, and this would become a pivotal tool for a
> subset of those.
> If not directly available, then a wishlist addition, perhaps?   
> Something like:
> zonesel [within|beyond] [+/- angstroms] [atom-spec]
> where the sign of the angstrom value denotes whether to include (+) or  
> exclude
> (-) the atoms in atom-spec.
> Cheers,
> Kenward Vaughan
> -- 
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