From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Aug 31 2011 - 06:22:04 CDT

On Aug 31, 2011, at 5:28 AM, ban arn <ban.arn_at_gmail.com> wrote:

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.

Please re-read the VMD documentation on the atom selection language. The
'and' is a logical and which means 'additional condition' but does not mean
'in addition'.

Axel

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.
>