[Chimera-users] interface residues

[Elaine Meng]

On Mar 17, 2008, at 9:56 AM, Francesco Malatesta wrote:

> Hello,
> could anyone help me out with this problem. I would like to  
> exclusively colour interface residues in a dimeric  protein  
> represented as spheres or surface. Is this possible?
> Thank you very much
> Francesco Malatesta
>

Hi Francesco,
Of course - there are so many different ways you could do it, I'm not  
sure where to start!   Also, I don't know if your structure is opened  
from two PDB files, or one PDB file with a different chain ID for  
each monomer.  You could do it either way, but in my examples I will  
assume you have one file with protein chains A and B like structure  
1tzz.  My examples are commands, but the same things can be done with  
menus and/or graphical interfaces (it would just take a lot more  
words to describe).

Possible ways to identify the residues:

(a) with a simple distance cutoff (Select... Zone... or in commands)
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ 
atom_spec.html#zones

command example:
color red :.a & :.b za<5

- that would color atoms in chain A that are within 5 angstroms of  
any atom in chain B; you can include a distance limit in many other  
commands, such as "select" "display" "repr sphere" "surface" etc.   
The "za" means atom-based cutoff, whereas "z" or "zr" means residue- 
based (would color whole residues with any atom within that  
distance).  You would then use a similar command for atoms in chain B  
close to atoms in chain A.

(b) with Find Clashes/Contacts (under Tools... Structure Analysis) or  
command "findclash"
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findclash/ 
findclash.html
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html

command example:
findclash :.a overlap -0.5 hb 0 makePseudobonds false select true
~select ~ :.b

- the first command selects any atoms outside of chain A that are  
close to chain A (any atoms with VDW surfaces within 0.5 angstroms of  
the VDW surfaces of atoms in chain A). The second command deselects  
atoms NOT in chain B, so what you have left are just the atoms in B  
that are close to A.  Then you can do what you want to the selected  
atoms with the Actions menu or other commands (including writing out  
a list of the atoms or residues).  Next, use similar steps to get  
atoms in chain A that are close to the atoms in chain B.

(c) with Intersurf (under Tools... Surface/Binding Analysis) or  
command "intersurf"
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/intersurf/ 
intersurf.html
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/intersurf.html

command example:
intersurf :.a :.b select true prune 10

That would select all the atoms from both chains found to form the  
interface.  See the links above for the algorithm.  The "prune"  
distance controls how far out to the sides the interface is computed  
and thus how many atoms will be selected.  Intersurf creates a  
special interface surface and opens a dialog for recoloring it based  
on the distances between the subunits. If you don't want that  
surface, you can just close it.

One other thing I should mention is that sometimes "surface" (display  
molecular surface, which is different than the special "intersurf"  
surfaces) will enclose multiple chains in the same surface when  
instead you wanted a separate surface for each chain.  You can tell  
Chimera to make separate surfaces, as explained here:
http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-February/ 
002382.html

I hope this helps,
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