VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jun 04 2003 - 16:23:06 CDT

Greg,
  Off the top of my head I don't know of any program that can calculate
the distance to a solvent accessible surface, however you could do this
yourself as follows:
  1) calculate surface using some program, getting a triangle mesh
     as the output

  2) put the triangles in a 3-D grid (to accelerate the search)
     and loop over the grid cells in order of increasing distance
     from your point of interest. For each grid cell, you could
     calculate distance by one of possibly several methods:
       A) intersect a ray with the triangles in the cell, taking the closest
          intersection as the distance. (ray shoots in the direction
          you mentioned below)
       B) choose the closest triangle facet vertex and use that
       C) some other simple method

VMD doesn't do this and I don't know anything that does, but it would
be a pretty easy program to write, perhaps it would take you a day
of work to write if you're familiar with this stuff if its as easy as
what I suggested above.

  John

On Wed, Jun 04, 2003 at 04:29:42PM -0400, Greg Moore wrote:
> Hello,
>
> I was hoping someone reading this list with more experience than I would
> know the answer to what I thought was a simple question. What I am trying
> to find is the distance from an atom in a protein to the solvent accessible
> surface (for a user input probe size) along a specified direction
> (typically ca -> cb). I was wondering if VMD (or maybe MSMS) can help me do
> this, or if anyone knows a better way. So far I've been able to get
> exposed/buried surface areas of each atom or residue with a number of
> programs, but not the distance. Thanks very much for any help,
>
> - Greg Moore
> glm113_at_psu.edu 

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NIH Resource for Macromolecular Modeling and Bioinformatics
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