From: Albers, Thomas (
Date: Thu Sep 14 2017 - 10:20:12 CDT

Thanks! It works!

It would be good to update the manual to include all the undocumented keywords for atom selection. Looking through AtomSel.C and AtomParser.y there's a few more, such as "ringsize" and "maxringsize".

From: Giacomo Fiorin <>
Sent: Wednesday, September 13, 2017 3:04 PM
To: Karteek Kumar
Cc: Albers, Thomas;
Subject: [EXTERNAL] Re: vmd-l: polar hydrogens

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I would look into using the withinbonds keyword that Josh mentioned a few days ago.

On Wed, Sep 13, 2017 at 1:39 PM, Karteek Kumar <<>> wrote:

Use a different name for polar hydrogen you want. Make a representation for those atoms (something like "name Hp")

Hope this helps.


On Wed, Sep 13, 2017 at 1:07 PM, Albers, Thomas <<>> wrote:


Is there any keyword in VMD that selects polar hydrogens (i.e. those bound to N, O and possibly S)?



Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD>>