[Chimera-users] robust molecular surface calculation

Francois Berenger berenger at riken.jp
Wed Feb 20 18:15:45 PST 2013


On 02/21/2013 05:44 AM, Hurt, Darrell (NIH/NIAID) [E] wrote:
> 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.

I think that's what MOE does also. That's a wise choice.

 > 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

If I can vote, then I vote against Pymol's surface.
It's just a hack, brute-force and inefficient algorithm (according to 
Waren Delano himself when you look into the subject on the net).

> 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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>>> Chimera-users at cgl.ucsf.edu
>>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>>>
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