From: Mark Cunningham (
Date: Fri Sep 09 2011 - 20:40:36 CDT


I thought you missed the obvious until I tried it myself but
chain A within 6 of chain B
throws an error. Nonetheless, you can get what you want with

(same fragment as all within 6 of chain B) and chain A

The first bit selects all of the whole fragments (residues) within 6 A of chain B
and the second bit outside the parentheses selects from that only what is in chain A.

Good luck,

From: [] On Behalf Of Irene Newhouse
Sent: Friday, September 09, 2011 4:19 PM
To: vmd list
Subject: vmd-l: Displaying residues on chain A within X of chain B

I'm trying to display the residues 'contacting' chain A on chain B of a protein [I'd be satisfied with setting a distance, as one does with 'within'] & I can't get the selection language to work in the graphical representations window. I've done some searching of the VMD-L archive, since people must want to do this, but I don't seem to have found the magic search terms. Using residue number isn't obvious, as the residues aren't numbered consecutively throughout the pdb file, but restart with each chain.

Irene Newhouse