VMD-L Mailing List

From: Greg Moore (glm113_at_psu.edu)
Date: Wed Jun 04 2003 - 15:29:42 CDT

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