VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Oct 23 2009 - 11:13:51 CDT

Hi,
  There's a minor bug in the current implementation that I'm working
on fixing, but in principle one ought to be able to do this with the
"withinbonds" selection, with something like this (where "A" and "C"
are some other selection text):

B atoms that are bonded to both A and C:
  withinbonds 1 of A and withinbonds 1 of C

The bug I'm working on fixing will prevent selections like the above
from working correctly at present, but I should have a fix for it
in the next few days and I can make it available in an alpha
version of VMD 1.8.8.

If you think of other bond-based selections that would be useful, let
me know and I'll see what I can do.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Oct 23, 2009 at 11:56:00AM -0400, Schmidt, Mike wrote:
> Hello,
>
>
>
> I was wondering if you can suggest a way to make a selection based on
> "bonded to" or consider this for a selection enhancement. Let me describe
> what I mean by "bonded to".
>
>
>
> With a hypothetical list of atoms bonded in this order, ABCDABDB, I'd like
> to find the B atoms that are bonded to both A and C for one case and later
> those B atoms bonded to A and D.
>
>
>
> I know I can come up with a tcl script that pulls the bond list for "type
> B" and then can retrieve by index a new selection to get the types of the
> atoms in the bond list.
>
>
>
> Any thoughts?
>
>
>
> Thanks,
>
> Mike 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078