[Chimera-users] zone command

[Elaine Meng]

Hi Francesco,
Maybe I am misunderstanding the question, but why not just select a  
zone around the ligand (with a command or "Select... Zone" in the  
menu), or use Find Clashes/Contacts (or the findclash command) to  
select residues in contact with the ligand?

<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#zones 
 >
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/menu.html#menuselect>

<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash.html 
 >
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html>

This is nearly the same topic as discussed last month in "pruning PDB":
<http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-October/003183.html 
 >

... you could write out a list of the selected residues (Actions...  
Write List or writesel command), undisplay the other residues, etc.
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/writesel.html>

The "Structural Analysis and Comparison" tutorial (Distances, H-Bonds,  
Contacts section) includes an example of using Find Clashes/Contacts  
to write a list of the residues in a ligand-binding site:

<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ 
squalene.html>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html#dists 
 >

Best,
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



On Nov 12, 2008, at 8:43 AM, Francesco Pietra wrote:

> A polypeptide was docked onto a protein that already carried ligands.
> Then, molecular dynamics of the complex was carried out. To do this, a
> single PDB file was created with the program ptraj of Amber.
>
> Although ptraj removes chain labels, TER lines, etc., renumbering all
> the residues in a single sequence, I know, from the ligand positions,
> the corresponding numbering for the chains and for the polypeptide.
>
> Which is the best procedure to map around certain groups of amino
> acids of the protein, i.e., those that constitute the
> experimentally-evaluated binding site? I want to take notice of which
> residues of the polypeptide are most involved in the binding.
>
> Thanks
>
> francesco pietra