[Chimera-users] Chimera SASA algorithm

Elaine Meng meng at cgl.ucsf.edu
Wed Nov 17 16:10:20 PST 2010

Hi Devin,
I assume you are talking about numerical errors?  My understanding is that these are exact, analytical values reported by the MSMS package:

In Chimera, molecular surfaces are created with embedded software from the MSMS package, described in:
Reduced surface: an efficient way to compute molecular surfaces. Sanner MF, Olson AJ, Spehner JC. Biopolymers. 1996 Mar;38(3):305-20. 

However, the MSMS calculation fails to generate a surface in some percentage of structures.  Probably more important than statistical numerical error bars is that different programs differ in the atomic radii used, and perhaps also in the treatment of interior bubbles.  There is no universally agreed-upon best set of atomic radii, whereas the probe radius is almost always 1.4 Angstroms.   Area magnitudes are best compared among different structures calculated by the same program, as opposed to completely different programs generally using different radii.

I faintly remember some publications comparing different surface calculation programs, but I believe they were focused on computational time and (complete) failure rate rather than a correct surface area, and these papers did not come out of our lab.  You might be able to find some with Pubmed searching.

While MSMS reports analytical values (at least, the results do not vary if you use a coarser triangulation of the displayed surface), other methods in Chimera of measuring surface area (command "measure area" and tools "Measure and Color Blobs" and "Measure Volume and Area") are based directly on the triangulation, and will approach analytical values as the triangles are made smaller and smaller.   However, the latter do not report SASA, only the MSMS-based methods do.

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

On Nov 17, 2010, at 1:54 PM, Devin McBride wrote:

> Hello,
> I have been using UCSF Chimera for a few years. I am currently reviewing the SASA algorithms by various molecular modeling software. I was wondering what the error associated with a given SASA calculation is? The algorithm has an error in the calculated SASA, but I was not able to find out what the error is. Thank you very much for your time and help.
> -- 
> Devin McBride
> Ph.D. Candidate
> Department of Bioengineering
> Bourns Hall A130
> University of California, Riverside
> Phone: (951) 742-3541
> Email: dmcbr001 at student.ucr.edu
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20101117/5f7dcfeb/attachment.html>

More information about the Chimera-users mailing list