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. _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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