VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Tue Aug 12 2008 - 10:53:35 CDT

On Tue, 12 Aug 2008, Roman Petrenko wrote:

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

no. you just do:

$sel frame $i
$sel update

voila!

a.
  

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