From: Vermaas, Joshua (
Date: Fri Feb 17 2017 - 18:38:01 CST

Hi Thomas,

I think that you actually want a larger radius, since you are clearly picking up small internal cavities due to a lack of hydrogens on your molecule. That being said, this protein is clearly some sort of channel, and so picking up surface atoms using VMD's algorithm is going to be VERY tricky indeed to get the pieces that line the pore without picking up internal cavities. Have you considered using alternative tools like CAVER, CHUNNEL, or HOLE? Unless of course you only care about the lipid interface. Then just crank up the radius and you'll be fine. :)


On 02/17/2017 02:44 PM, Albers, Thomas wrote:


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?