[Chimera-users] Question about Measure Volume and Area

Elaine Meng meng at cgl.ucsf.edu
Fri Aug 15 11:12:54 PDT 2008

Hi Patrick,
Thought I should mention that "Area/Volume from Web" (actually the  
Web server it accesses
<http://helixweb.nih.gov/structbio/basic.html> ) is mainly  
parametrized to work on proteins, possibly nucleic acids.  I would  
interpret the results with caution, as I don't know how it figures  
out the atom types (and thus VDW radii) in arbitrary molecules.

On your structure, I tried the "Accessible surface (Gerstein)" option  
directly at the server, probe radius 1.4, and got values per atom  
plus this total:
Chain X
Residue     Exposed Surface Area (Å2)
    1        1918.02

(default probe radius is 1.4).  Note "solvent-accessible  
surface" (SAS) area is where the center of the probe goes, not the  
same as the "solvent-excluded surface" (SES) comprised of probe  
contact and reentrant surface, and is expected to be much larger as  
it is a probe radius farther out.  The surface in Chimera is the SES.

Then I tried "Surfaces (MSMS)", probe radius 1.4, atoms+hetatms, and  
got this:

     Comp. probe_radius,   reent,    toric,   contact    SES       SAS
       0       1.400     174.758   554.648   491.498  1220.904  1600.598

... so this SES is fairly consistent with but larger than the value  
of 1174 you got in Chimera, probably because this server MSMS  
calculation used a larger VDW radius for the carbons. The SAS  
difference versus the Gerstein method is >300 - maybe the Gerstein  
calculation used an even larger VDW radius.

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 Aug 15, 2008, at 8:26 AM, Patrick Redmill wrote:

> Thanks guys!,
>    What you're saying makes a lot of sense actually. Now that you  
> mention it, I am sure both surfaces are being measured. This is the  
> fattest (closed) particle I have, thus, it makes sense that the  
> interior surface was measured for that one but not the others. I'll  
> definitely try out the "Measure and Color Blobs" and "Area/Volume  
> from the web." Thanks again!
> ~Patrick

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