From: Irene Newhouse (einew_at_hotmail.com)
Date: Sat Sep 10 2011 - 00:33:25 CDT

Thanks so much! Irene
 From: cunningham_at_utpa.edu
To: einew_at_hotmail.com
CC: vmd-l_at_ks.uiuc.edu
Subject: RE: vmd-l: Displaying residues on chain A within X of chain B
Date: Sat, 10 Sep 2011 01:40:36 +0000

Irene: I thought you missed the obvious until I tried it myself butchain A within 6 of chain Bthrows 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 Band the second bit outside the parentheses selects from that only what is in chain A. Good luck, MarkFrom: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] 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.
 
Thanks!
Irene Newhouse