VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Oct 14 2016 - 10:05:05 CDT

Hi,
  It wasn't clear to me if in Francesca's case she was modifying bonds
prior to the selection. So long as the VMD structure analysis is
up-to-date at the time the selection is done (e.g. if one would change
any bonds interactively or the like, you would have to do a "mol reanalyze"),
then the "fragment" selection Axel suggests would be faster than the
"withinbonds" suggestion I gave earlier. The "withinbonds" selection
has to walk the bondlist during selection, whereas "fragment" does not,
so "fragment" would be much faster if you're not modifying anything in the
structure.

Cheers,
  John

On Fri, Oct 14, 2016 at 10:52:54AM -0400, Axel Kohlmeyer wrote:
> On Fri, Oct 14, 2016 at 6:39 AM, Francesca Lønstad Bleken
> <FrancescaL.Bleken_at_sintef.no> wrote:
> > Hi,
> >
> >
> >
> > Is there a way to select atoms according to bonding in the sense "select a
> > molecule"
>
> you can select by the "fragment" property, which is generated by VMD
> based on connectivity.
>
> axel.
>
>
> >
> >
> >
> > 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
> >
> >
>
>
>
> --
> 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. 

-- 
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/