From: Axel Kohlmeyer (
Date: Tue Aug 30 2011 - 13:19:46 CDT

On Tue, Aug 30, 2011 at 1:14 PM, ban arn <> 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.


> Many Thanks
> Balaji

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.