From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Oct 23 2009 - 13:39:08 CDT

Mike,
  I've posted a test version of VMD (1.8.8 alpha 4) that includes
the fix I mentioned for the withinbonds selection. It's available
in the VMD public project in biocore:
  http://www.ks.uiuc.edu/Research/vmd/alpha/

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Oct 23, 2009 at 11:13:50AM -0500, John Stone wrote:
> 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

-- 
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