[Chimera-users] Unit of electrostatic surface coloring within Chimera

Elaine Meng meng at cgl.ucsf.edu
Tue Feb 19 10:04:06 PST 2013


Hi Florian,
Chimera simply takes the values directly from the map, and the units of the map depend on which program is used.

Looking at the APBS help, the units of APBS output appear to be kT/e:
<http://www.poissonboltzmann.org/apbs/frequently-asked-questions/what-are-the-units-of-electrostatic-potential>

At 298K, 10 kT/e is approximately 5.93 kcal/(mol.e).

I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Feb 18, 2013, at 5:09 AM, Florian.Capito at external.merckgroup.com wrote:

> To whom it may concern,
> 
> I am using Chimera to color surfaces of proteins according to electrostatic
> potential files calculated by APBS.
> Now, in Chimera, there is the option to select a threshold, e.g. at which
> value the surface should be colored in red and at which value it is colored
> in blue.
> 
> Now i would like to know in which unit this threshold works? Is it kcal
> (mol·e)-1?
> 
> While this has been described for the Coloumbic surface coloring within
> Chimera Help, I could not find any explanation for this in the help menu,
> when loading external APBS potential files into Chimera.
> 
> Thank You very much for Your time and help!!!
> 
> 
> Mit freundlichen Grüssen/ With best regards
> 
> Florian Capito
> MM-PTD-New Downstream Darmstadt
> Location A17/217
> Postcode: A046/509
> Phone: +49 6151 72-7168
> Email: florian.capito at external.merckgroup.com
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