VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Oct 14 2016 - 09:41:12 CDT

Hi,
  You can use "withinbonds N" to select atoms that are within a certain number
(N) of bond traversals from the other part of the selection. If you were trying
to select anything that is part of your "new molecule", I suppose you could
do a withinbonds selection with a very larger cutoff count (equal to the
total number of atoms for example) and you would get back everything in the
"new molecule" attached to the starting selection. I haven't personally
tried it with a huge bond traversal count value, but I would expect
it to work fine because the selection algorithm is designed to be
reasonably efficient and avoids various redundant traversals by marking
its traversal paths as it goes.

Cheers
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Oct 14, 2016 at 09:30:56AM +0000, Francesca Lønstad Bleken wrote:
> Hi,
>
>
>
> Is there a way to select atoms according to bonding in the sense "select a
> molecule"
>
>
>
> I have used topotools to clear and guess new bonds, and visually this look
> ok, but I would like to select one and one molecule.
>
> With getbonds I can get the list of all bonds, but since the system is big
> I would like to know if there are any solutions or suggestions for how to
> select just one of the "new" molecules.
>
>
>
> Best regards,
>
> Francesca
>
>
>
> 

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