VMD-L Mailing List

From: Roman Petrenko (rpetrenko_at_gmail.com)
Date: Tue Aug 12 2008 - 10:52:32 CDT

thanks, that works. "update selection every frame" was the missing element.
so, i assume that if i want to have the same feature in a script, then
i should place [atomselect] command inside the loop over all frames,
is it right?

On Tue, Aug 12, 2008 at 11:37 AM, Axel Kohlmeyer
<akohlmey_at_cmm.chem.upenn.edu> wrote:
> On Tue, 12 Aug 2008, Roman Petrenko wrote:
>
> RP> Dear all,
> RP> i am making a movie in vmd and want to display only those hydrogen
> RP> bonds which are formed between a protein and water molecules
> RP> (protein-protein HB are ok as well).
> RP> is there any way to do it?
>
> how about selecting "within 3.0 of protein" for the hbonds
> representation? you also want to enable "Update Selection Every Frame"
> in the Trajectory tab...
>
> cheers,
>
> axel.
>
>
> RP> the problem is if i display only protein (no water) and choose Hbonds
> RP> representation, then only protein-protein HB are displayed.
> RP> if i display everything (protein+water), then protein-water HBs are
> RP> visually hidden by numerous useless hydrogen bonds between water
> RP> molecules.
> RP>
> RP>
>
> --
> =======================================================================
> Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
> Center for Molecular Modeling -- University of Pennsylvania
> Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
> tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
> =======================================================================
> If you make something idiot-proof, the universe creates a better idiot.
> 

-- 
Roman Petrenko.
Physics Department
University of Cincinnati