From: Vermaas, Josh (
Date: Tue Aug 16 2022 - 12:53:40 CDT

Hi Caleb,

The way I’d break it down is possibly a bit counter-intuitive. The “measure contacts” command will give you the pairs that you are looking for (

So “measure contacts 3.0 [atomselect top “name OG”]” in the tkCon will get you a list at the current frame, and you could script this to give you the indices at a particular frame, and change the representations accordingly.


From: <> on behalf of "Huang, Caleb" <cjhuang_at_UTMB.EDU>
Date: Tuesday, August 16, 2022 at 1:37 PM
To: "" <>
Subject: vmd-l: atomselect for interacting hydroxyl groups


I'd like to select all atoms that are within 3A of another atom with the same identifier. More specifically, I want to select all serine oxygen "OG" that are within 3A of a different "OG". The following commands command doesn't work, as it selects all OGs, not just OG's that are within 3A of other OGs: name OG and within 3 of (name OG). I'm thinking that this what the command should look like: name OG and within 3 of (DIFFERENT name OG) -- except I'm not sure how to specify "different" OG with the same identifier.
Any help would be appreciated!