[Chimera-users] robust molecular surface calculation

[Hurt, Darrell (NIH/NIAID) [E]]

Hi Conrad,

I'm sure that you are much better versed in and better positioned to chose
than I. However, here are some thoughts:

First, is it critical that the mesh be triangular? Or can it be made of
quads or n-gons? How important is the regularity of the mesh? A Voronoi
surface implementation would be interesting, but it might present more
difficulties than it is worth when trying to map bio/chem/physical
properties to the surface.

VMD uses isosurfaces extracted from volumetric Gaussian density maps
("quicksurf") to create surfaces fast enough to be recalculated on the fly
for animating trajectories. This is similar to the tip that Elaine and Tom
posted about "faking" a molecular surface when MSMS fails:
http://www.ks.uiuc.edu/Research/vmd/current/ug/node72.html
http://plato.cgl.ucsf.edu/pipermail/chimera-users/2012-January/007048.html

The BioBlender project calls PyMOL for generation of its surfaces. As you
know, PyMOL surfaces are distinctive and attractive, but not much faster
than MSMS:
http://bioblender.eu
http://www.scivis.ifc.cnr.it/images/stories/PDFarticle/1009.4674.pdf
http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg06658.html

I like the spherical harmonics approach of Bruce Duncan, but I suspect
that Chimera already incorporates this technique in the "Multiscale
Models" module.
http://mgl.scripps.edu/people/bsd/cv/cv.html

I wonder if "Surface Racer" could be implemented somehow. It seems very
fast and it calculates per-residue surface areas, just like the current
MSMS implementation:
http://apps.phar.umich.edu/tsodikovlab/index_files/Page756.htm

OK, I'm tapped out for now...

Cheers,
Darrell


Darrell Hurt, Ph.D.
Section Head, Computational Biology
Bioinformatics and Computational Biosciences Branch (BCBB)
OCICB/OSMO/OD/NIAID/NIH
 
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On 2/20/13 12:24 PM, "Conrad Huang" <conrad at cgl.ucsf.edu> wrote:

>We are starting work on Chimera 2, which will replace the aging user
>interface (Tk) and legacy graphics library calls (OpenGL 1 and 2).  We
>will probably replace MSMS as part of that work.
>
>We have examined a number of alternative algorithms, most of which do
>not compute analytical solutions as MSMS does.  However, the numerical
>algorithms seem acceptable and are more efficient, so we will probably
>go with one of them.  If there is a favorite molecular surface algorithm
>that you'd like to see in Chimera, please let us know (both which
>algorithm and why, which would greatly help us evaluate their relative
>strengths and weaknesses).
>
>Conrad
>
>On 2/19/13 6:10 PM, Francois Berenger wrote:
>> Hello,
>>
>> Is there any plan to plug some alternative molecular surface calculation
>> algorithm into chimera?
>>
>> I have seen some interesting articles about isosurface and gaussian
>> density functions:
>>
>> "Yu, Z., Jacobson, M. P. and Friesner, R. A. (2006), What role do
>> surfaces play in GB models? A new-generation of surface-generalized born
>> model based on a novel gaussian surface for biomolecules. J. Comput.
>> Chem., 27: 72­89. doi: 10.1002/jcc.20307"
>>
>> "What role do surfaces play in GB models? A new-generation of
>> surface-generalized born model based on a novel gaussian surface for
>> biomolecules
>> DOI: 10.1002/jcc.20307"
>> http://onlinelibrary.wiley.com/doi/10.1002/jcc.20307/abstract
>>
>> The algorithm looks simple, robust and even parallelizable.
>> I kind of guess that's the algorithm used in MOE when I look
>> at their triangulation.
>>
>> Regards,
>> Francois.
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>>
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