From: Jeremías Corradi (
Date: Tue Apr 22 2014 - 10:08:58 CDT

sorry Axel to bother, i don't want a "personal trainer", the only thing i'm
looking for is just some guide how to show the h-bonds, or other
interactions, because the guide i found on the web and other messages in the
list were not clear enough for me...
after doing that i will use VMD to get the "nice picture" i want combined
with other programs... like PovRay...


-----Mensaje original-----
From: Axel Kohlmeyer
Sent: Tuesday, April 22, 2014 11:50 AM
To: Jeremías Corradi
Cc: Vmd l
Subject: Re: vmd-l: ligand-protein bonds representation

On Tue, Apr 22, 2014 at 9:36 AM, Jeremías Corradi <>
> Hi, i want to make a nice figure from a docking result and i need help
> with
> H-bond, pi-pi and cation-pi representations in VMD, are they possible? can
> somebody give me a step-by-step tutorial how to do this???

are you saying you want a personal trainer?
don't think you'll find one unless you offer some compensation worth
the effort. remember that you want to be taught how to do some custom
visualization that probably not a lot of people have done and thus
whoever would help you will first have to figure out how to do exactly
what you want.

on the other hand, you can just go through the existing visualization
tutorials and teach yourself how VMD works and particularly how you
can add custom graphics elements to a representation and then not only
have your immediate problem solved, but acquired a useful skill for
the future.

please also note that many *very* nice images are composites that take
an image rendered with a molecular visualization tool and then augment
it with a tool like gimp or photoshop.

finally, very nice pictures don't come automatically. they are usually
the result of some experimentation, experience and inspiration...


> thank you very much in advance
> Jeremías
> Dr. Bioq. Jeremías Corradi
> Bahía Blanca - Argentina

Dr. Axel Kohlmeyer
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.