VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Mar 25 2015 - 12:43:28 CDT

On Wed, Mar 25, 2015 at 12:22 PM, Josh Vermaas <vermaas2_at_illinois.edu> wrote:
> Hi Mike,
> You need to cook up a selection that only includes the in between bits. How
> about "sidechain and ((exwithin 3.5 of chain A) or (exwithin 3.5 of chain
> B))"? This has three parts. One to pick up only the sidechains, and then two
> more that pick stuff near the chains that aren't the chains themselves.
> There are other alternatives, and perhaps others will chime in.

as mike stated, you can cook up as smart a selection as you want, for
as long as VMD only accepts a single selection, it won't work for
cases where you only want to show A-B and not A-A or B-B (dynamic
bonds or polyhedra have the same problem). the alternative requires
some hacking in VMD itself and has been put on john's TODO list long
ago. it touches parts of the code that affect *all* users, so he is
very careful with this and thus it so far has not yet managed to be
important enough to make it to the top of this list.

axel.

> -Josh
>
> On Mar 25, 2015 9:30 AM, "Dolan, Michael A. (NIH/NIAID) [C]"
> <dolanmi_at_niaid.nih.gov> wrote:
>
> Hello,
>
>
>
> I’ve seen some posts addressing this question before, but has there been any
> changes in the code to address the possibility of being able to show only
> those H-bonds occurring between two chains or segments?
>
>
>
> Something like the following selection will show H-bonds between chain A and
> B, but also within chain A and B:
>
>
>
> chain A B
>
>
>
> I guess that there is no Boolean-like way to do this. Perhaps the addition
> of a ‘between’ option….
>
>
>
> Thanks!
>
> Mike 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.