[Chimera-users] Positioning of water molecules in a protein

[Elaine Meng]

Hi John,
Chimera has many features for examining structural details and interactions among 
and between sets of atoms.  There are so many possibilities I'm at a loss as to 
how to answer this question.  I'll try to touch on a few different things and 
provide links to where you can learn more.  

Maybe the "Structure Analysis and Comparison" tutorial would be useful:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html>

You can examine all the contacts and/or H-bonds made by some set of atoms.
  
There is a "Find Clashes/Contacts" tool and corresponding "findclash" command,
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash.html>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html> 
and a "FindHBond" tool and corresponding "findhbond" command.
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbond.html>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/hbonds.html>

Command-line specifications could use specific residue numbers for one or more 
waters, or "solvent" to mean all waters, or "sel" to mean the current selection.
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html>

You can look at all atoms within a particular cutoff distance of some other set
of atoms.  Zones can be specified in the command line, or you can select something
and then use the menu item "Select... Zone" to also select atoms within a cutoff 
distance of the initial selection. Example commands:
   rlabel solvent zr<4.5     
(residue-label all residues within 4.5 ang of any solvent atom)
   color red :453.a za<5    
(color red all atoms within 5 ang of residue 453 in chain A)
   select sel zr<8
(select all residues with any atom within 8 ang of current selection)
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#zones>

You can measure distances, angles, ...
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Aug 18, 2010, at 8:19 AM, Beale, John wrote:

> Is there a way to use Chimera to determine what atoms/groups in a protein are closest to a particular water molecule? I have an x-ray structure that is solvated. I would like to determine the positions of the water molecules in the x-ray structure and compare these to the water molecule positions after molecular dynamics.
> Thanks! 
> John