[Chimera-users] robust molecular surface calculation

Conrad Huang 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).

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


More information about the Chimera-users mailing list