[Chimera-users] water around protein

Elaine Meng meng at cgl.ucsf.edu
Fri May 25 09:32:53 PDT 2012

Hi Bala,
With findclash (or GUI Find Clashes/Contacts) you can identify contacts between two groups of atoms using their VDW radii.  You would specify "overlap" cutoff for the overlap between the VDW surfaces.  For example, overlap 1.0 would be intersection of VDW surfaces of 1 angstrom (clashing), overlap 0.0 would be VDW surfaces exactly touching, overlap -1.0 would be VDW surfaces 1 angstrom apart.  Normally H-bonding pairs are allowed to come closer, so their VDW sizes are reduced by an "allowance" in that case, but you can turn that off if you prefer.

Here is a simple example, but you should take a look at the documentation to see the many options.  The example is to identify waters with VDW surfaces within 0.5 angstroms of protein VDW surface, without reducing the VDW radii in H-bonding pairs.  In my case, the waters are named HOH.

findc :hoh test protein overlap -.5 hbond 0 select true

See manual page for command or GUI:

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

On May 25, 2012, at 4:07 AM, Bala subramanian wrote:

> Friends,
> I guess when i select no. of water as "sel ::WAT & protein z<3", i the distance of water is chosen as distance from atom protein atom centres. Instead i want to calculate no. of water around the protein Vdw surface with same distance value. Any idea would be of great help. 
> Thanks,
> Bala

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