[Chimera-users] accessible surface area for electron density maps

[Elaine Meng]

Hi David,
As soon as you show a molecular surface, both the total solvent- 
excluded (molecular surface by Richards definition) and solvent- 
accessible areas are reported in the Reply Log.  It has been like  
that since before the July 2008 release.

The surface that is actually displayed is the solvent-excluded surface.

You can adjust parameters that affect the results such as probe  
radius and atomic radii, but the defaults are reasonable.

The area values are also assigned as per-atom and per-residue  
attributes named areaSES and areaSAS, so you can use Attribute  
Calculator to get sums over subparts of the surface.

For details, see this page and links therein:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/ 
representation.html#surfaces>

I hope this helps,
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 Mar 27, 2009, at 8:58 AM, David Chenoweth wrote:

> Hi Elaine and Murali,
>
> I have a similar problem that I've been trying to resolve.  
> Calculating the accessible surface or solvent accessible surface is  
> also something I've been interested in doing with Chimera but I  
> don't think the area of the molecular surface is the same as the  
> solvent accessible surface area. I believe that accessible surface  
> comes from the locus of the center of a spherical probe as it rolls  
> over the Van der Waals surface of a molecule. The molecular surface  
> uses the locus of the inward facing spherical probe. They both  
> depend on the spherical probe size which is set to the appropriate  
> solvent molecule. Can you tell me which of these two methods  
> Chimera is using when it calculates the area (if either)? Is there  
> a way to calculate the solvent accessible surface area of a  
> molecule with Chimera or some way to manipulate the current area  
> calculator to give this value? I also think that depending on the  
> quality of the electron density map one could get very different  
> results for this calculation (especially if there is missing  
> electron density or at different map contour values). If anyone has  
> any advice for the best way to calculate solvent accessible surface  
> area I would really appreciate the help.
>
> Thanks,
> Dave Chenoweth