[Chimera-users] robust molecular surface calculation
conrad at cgl.ucsf.edu
Wed Feb 20 09:24:50 PST 2013
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).
On 2/19/13 6:10 PM, Francois Berenger wrote:
> 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
> DOI: 10.1002/jcc.20307"
> 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.
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