[Chimera-users] Chimera SASA algorithm

[Devin McBride]

Hello Elaine,

Thank you very much for your help.

Devin McBride

On Wed, Nov 17, 2010 at 4:10 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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 <http://www.scripps.edu/~sanner/html/msms_home.html>, described
> in:
>
> Reduced surface: an efficient way to compute molecular surfaces.<http://www.ncbi.nlm.nih.gov/pubmed/8906967>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
>  -----
> 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
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>
>


-- 
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
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