[Chimera-users] Distance Grid SES calculation available?

Tom Goddard goddard at sonic.net
Tue Jan 6 12:01:40 PST 2015


Hi Darrell,

  Ok, there is a secret Chimera 1 option to the surface command to let you use the distance grid SES calculation:

	surface #0 grid 0.5

The value of the grid option is the grid spacing and 0.5 Angstroms is reasonable, smaller values will produce a more finely triangulated surface.  This surface cannot be colored to match the atom colors in the same way as a normal molecular surface because it lacks an association between surface points and atoms (although the color zone tool can get the same effect if you need it).  This is an undocumented feature because if we add all our cool new features to Chimera 1 then we will never have time to get Chimera 2 produced.  But since you need it here it is.

	Tom



> On Jan 5, 2015, at 8:49 PM, Hurt, Darrell (NIH/NIAID) [E] <darrellh at niaid.nih.gov> wrote:
> 
> 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
> 
> --
> Darrell Hurt, Ph.D.
> Section Head, Computational Biology
> Bioinformatics and Computational Biosciences Branch (BCBB)
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