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