VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Oct 14 2016 - 09:52:54 CDT

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.