[Chimera-users] Distance Grid SES calculation available?

Hurt, Darrell (NIH/NIAID) [E] darrellh at niaid.nih.gov
Mon Jan 5 20:49:07 PST 2015


Hi Chimera friends,

This question is probably for Tom Goddard, but I'm happy to hear from anyone. I'm really interested in using Tom's code for "distance grid SES" calculations as described here:
http://www.cgl.ucsf.edu/chimera/data/surface-oct2013/surface.html

The above page suggests that this code will be part of Chimera 2, but I'm wondering if it is available now for surface calculations. Too many of my surface calculations are failing for our production server using Chimera. This would help immensely. Molmap is a decent alternative in some instances, but for my purposes, distance grid calculations are going to be more MSMS-like, which will be a better solution (cf. the description on the page comparing the internal pockets formed by molmap vs MSMS surfaces).

Is there some way to call the routine, especially in a script? Python maybe?

Thanks,
Darrell

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Darrell Hurt, Ph.D.
Section Head, Computational Biology
Bioinformatics and Computational Biosciences Branch (BCBB)
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