VMD-L Mailing List

From: Mark Cunningham (cunningham_at_utpa.edu)
Date: Fri Sep 09 2011 - 20:40:36 CDT

Irene:

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,

Mark
From: 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