VMD-L Mailing List

From: ban arn (ban.arn_at_gmail.com)
Date: Wed Aug 31 2011 - 04:28:35 CDT

Dear VMD users

Thanks for suggestion.

For display of polar hydrogens, for example i used command as "resid 142 and
polar hydrogens", it displays polar hydrogens as atoms.

The bonds are not connected.

For undisplaying non polar hydrogens, i used command as "resid 142 and not
all hydrogens" it doesnot work whereas "resid 142 and noH" hides all
hydroegns.

Kindly advice.

Many Thanks
Balaji

On Tue, Aug 30, 2011 at 7:19 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> On Tue, Aug 30, 2011 at 1:14 PM, ban arn <ban.arn_at_gmail.com> wrote:
> > Dear VMD user
> >
> > I would like to display water within 3 of ligand.
> >
> > I'm using command as " waters within 3 of resname UNK".
> >
> > It shows only hydrogens for some of the water molecules instead of full
> > molecule.
>
>
> > How to dispaly the full molecule if its selected within 3 A.
>
> try: "same fragment as (water and (within 3.0 of resname UNK))"
>
> > I would also like to know the command for how to undisplay the non-polar
> > hydrogens in VMD.
>
> VMD, like most software, has no intelligence and no common sense.
> you should always keep that in mind when asking questions like this.
>
> thus in order to select or deselect something, there has to be
> some indication. the logic if the atom selection can be turned into
> rather complex expressions, though. for example if you don't know
> how to specify the non-polar hydrogen atoms, you can just not display
> _all_ hydrogens and the "or" that selection with recognizable polar
> hydrogen and so on.
>
> axel.
>
> > Many Thanks
> > Balaji
> >
> >
> >
> >
> >
>
>
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com http://goo.gl/1wk0
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.
>