From: Albers, Thomas (
Date: Fri Feb 17 2017 - 14:47:07 CST


I am having problems getting the "measure surface" command to work properly and return only atoms that are close to the protein's surface.

% mol pdbload 1TNF

% set protein [atomselect top protein]

% set surf [measure surface $protein 1.5 3.0 2.0]

% $protein set beta 0

% foreach s $surf {set sel [atomselect top "index $s"]; $sel set beta 1; $sel delete}

You'd think that a reasonably tight spacing of grid points combined with a generous exclusion radius would return only atoms on the surface of the protein - however this isn't the case, many atoms inside the selection are picked as well. What would be a sensible set of parameters here?