[Chimera-users] robust molecular surface calculation

Francois Berenger berenger at riken.jp
Wed Feb 20 18:02:38 PST 2013


On 02/21/2013 02:24 AM, Conrad Huang 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.

At least, there should be alternatives to MSMS.

> 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).

The first one I referenced looks ideal (gaussian, isosurface and 
marching cubes).

I think I saw some papers where people derived analytical formulas
to compute surface and volume fast for molecules describbed with gaussians.

If I was to do the job, I would run far away from Connolly-style
surfaces (because it is hell to implement and you need
CGAL to implement it if you want something robust).

> 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: 72–89. 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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