VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Jul 21 2008 - 10:22:51 CDT

Beyond the reply that Eduard already sent, I just wanted to mention
that you can use a script to compute SASA per residue, assign the
per-residue SASA to "beta" or "user" (Just as an example. You could
just as easily use any of the per-atom fields) and then use a selection
like:
  beta > 0

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sun, Jul 20, 2008 at 05:28:04PM -0400, Christopher Gillespie wrote:
> Hello,
> I am trying to generate some rdfs for systems that I have already run. I
> want to do these using the protein surface as one selection. I know that
> using the selection "Protein and Surface" only implies "Not Buried" which
> removes hydrophobic residues from the selection set, but I want to see the
> actual atoms, including any hydrophobic ones that have at least some SASA,
> while also not including polar atoms that are actually buried, e.g. at the
> dimer interface. I know it may not be exactly correct since I should have
> to determine the SASA for each frame, but to make this doable in a
> reasonable amount of time and since my protein has an average RMSD of ~1.2A
> the atoms that make up the set from frame 0 should not deviate that much, I
> assume.
>
> So does anyone know how to define a selection of SASA > 0 atoms for use in
> gofr?
>
> Thanks
>
> Chris 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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