[Chimera-users] accessible surface area for electron density maps
meng at cgl.ucsf.edu
Fri Mar 27 10:12:52 PDT 2009
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:
I hope this helps,
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
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.
> Dave Chenoweth
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