VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Dec 01 2003 - 15:37:46 CST

Dear Tyler,
  You can "screen" for almost any atom property you like through the use
of the VMD atom selection language. In your case, you could use something
like "radius > 1.1" or something like that, whatever radius cutoff you like.
Give this a try in the graphical representations window and you should be able
to immediately experiment with various selections. I'd suggest building the
selection using a "lines" rep first, so you can see results quickly, then
re-try your MSMS surface when you're satisfied. MSMS uses its own radii,
which is why you're getting different results when you run it by hand BTW.
(Unless you've written your own front-end rather than using the normal method
 they recommend)

Give that a try and let us knwo if you need more help tuning this up.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Sun, Nov 23, 2003 at 03:18:10PM -0700, Tyler Luchko wrote:
> Hello,
>
> I've written a script to set all atom radii to their CHARMM 27
> Lennard-Jones radii and have run into a problem with MSMS. Unless I set
> the probe radius quite large, typically > 2, MSMS returns no surface. I
> have run MSMS on the same structures myself using CHARMM radii without a
> problem. I suspect that with VMD the problem lies in that many of the
> hydrogens have radii so small that they are completely buried inside
> another atom. Would it be possible to screen for such atoms and not
> submit them?
>
> Thank you,
>
> Tyler
>
> ________TyLer_LuchKo__::__MaSters_StuDent__->>__DePartMent_Of_PhysIcs_________
> _______UnIVerSiTy_Of_AlBerTa__->>__EdMonTon__->>__AlBerTa__->>__CanADa________
> ____http://Phys.UAlBerTa.Ca/______________________tluchko@Phys.UAlBerTa.Ca____
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-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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