[Chimera-users] zone command between proteins

[Elaine Meng]

Hi Francesco,
You would have to use residue numbers and/or chain IDs.  Actually the  
peptide is also "protein" (at least the standard residues) so you  
would not want to use that specifier anyway.  If your peptide was  
chain B and the protein was chain C, for example:

sel :.c & :.b z<5

Or if everything was chain A and your protein is residue numbers 3-455  
and the peptide is residues number 456-462:

sel :3-455.a & :456-462.a z<5

There are several ways to figure out the numbers and chain IDs,  
including looking at the balloon help that pops up when you hold the  
cursor over some atoms on the screen, or using the Sequence tool, or  
using a text-editor to look at the PDB file.

See "atom specification" for details on using model, residue, chain  
IDs etc. in the command line.
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html 
 >

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 Sep 12, 2010, at 7:28 AM, Francesco Pietra wrote:

> Hello:
> How to map the residues at a given distance (<5A) between a protein
> and its 5-residues peptide ligand? I could only use the zone command
> for a non-standard residue in the peptide:
>
> sel protein & :non-standard_residuename_of_peptide
>
> All other peptide residues are standard residues.
>
> thanks
> francesco pietra