[Chimera-users] Hydrogen Atoms

Thiruvarangan Ramaraj thiruvaranganr at yahoo.com
Mon Feb 15 00:26:36 PST 2010

Thanks Elaine.

So Chimera doesn't automatically add hydrogen atoms during the surface calculations, unless the user adds it



--- On Sun, 2/14/10, Elaine Meng <meng at cgl.ucsf.edu> wrote:

From: Elaine Meng <meng at cgl.ucsf.edu>
Subject: Re: Hydrogen Atoms
To: "Thiruvarangan Ramaraj" <thiruvaranganr at yahoo.com>
Cc: "Chimera BB" <chimera-users at cgl.ucsf.edu>
Date: Sunday, February 14, 2010, 1:41 PM

On Feb 14, 2010, at 11:31 AM, Thiruvarangan Ramaraj wrote:

> Hi Elaine,
> I am working on calculating the Solvent accessible Surface Area on the antigen interaction region. I am confused about adding/removing hydrogen's, my question is will there be a change in SASA if you have or not have  hydrogen's atoms added.
> Thank You.
> -Thiru

Hi Thiru,
Yes, it will be different with and without hydrogen, because the molecule is treated as a set of spheres where each atom is a sphere.  There will be more small bumps on the surface when there are hydrogens.  Also, the radii of the other atoms may change because there are different defaults for structures with and without hydrogens, as described here:


I think surface area calculations are usually done on structures without hydrogens.
I hope this helps,
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

P.S. you may want to use "measure buriedArea" (or maybe you are already doing that):

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