[Chimera-users] command line zone selection?

[Elaine Meng]

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):
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ 
frameatom_spec.html

It can be confusing, so feel free to write back if you have problems  
generating the command needed in your particular situation!
Best,
Elaine
-----
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
                      http://www.cgl.ucsf.edu/home/meng/index.html


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
> -- 
>                                        .'^~;,_
> Dr. Kenward Vaughan                    `:,'~~~~~
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