[Chimera-users] Showing Binding surface

Elaine Meng meng at cgl.ucsf.edu
Thu Jan 10 16:10:48 PST 2013


Hi Bobo,
The molecular surface areas (SASA, SESA) are calculated analytically by the MSMS  module.

"Measure Volume and Area" does not perform any analytical calculation, it just adds up the areas of the flat triangles that make up the surface.  The smaller the triangles (higher vertex density), the closer to the analytical value.

The "Measure Volume and Area" manual page mentions this a little bit, near the top...
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/measurevol/measurevol.html>

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

On Jan 10, 2013, at 4:03 PM, Bobo Dang wrote:

> Hey Elaine,
> 
> You are right, I think I didn't make it clear before.
> 
> Here is where I got the different value:
> 
>  after surfcat, I selected the surface for d chain and use "measure volume and area" in tools->surface and binding assays, then I got a area value, that's where the difference come from. 
> 
> the function "measure volume and area" just gives a volume and a area value, it doesn't distinguish SAS or SES.
> 
> I checked the manual guide more carefully, it says this function gives the "total surface area of a surface model", but again I don't really understand how chimera define the model.
> 
> Thanks for your great help.
> 
> bobo




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