VMD-L Mailing List

From: poker_at_physics.usyd.edu.au
Date: Tue Aug 25 2009 - 22:13:26 CDT

I've been wondering - is there a way to select just the polar hydrogens in VMD?

This is what I'm after - I'm inspecting a semi-buried portion of a protein with
a h-bonding network, and wish to visualise what the sidechains are doing.
However, I've got an all-atom model where the aliphatic/aromatic hydrogens are
cluttering up the display, and I haven't found an easy solution to choose only
the polar hydrogens that can h-bond.

I guess this is a feature request for a selection keyword that includes only
polar hydrogens?

thanks,
P.