[Chimera-users] Hydrogen Atoms

[Elaine Meng]

On Feb 14, 2010, at 11:31 AM, Thiruvarangan Ramaraj wrote:

> Hi Elaine,
> I am working on calculating the Solvent accessible Surface Area on  
> the antigen interaction region. I am confused about adding/removing  
> hydrogen's, my question is will there be a change in SASA if you  
> have or not have  hydrogen's atoms added.
> Thank You.
> -Thiru
>

Hi Thiru,
Yes, it will be different with and without hydrogen, because the  
molecule is treated as a set of spheres where each atom is a sphere.   
There will be more small bumps on the surface when there are  
hydrogens.  Also, the radii of the other atoms may change because  
there are different defaults for structures with and without  
hydrogens, as described here:

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

I think surface area calculations are usually done on structures  
without hydrogens.
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

P.S. you may want to use "measure buriedArea" (or maybe you are  
already doing that):
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#buriedArea 
 >