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...> 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@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@external.merckgroup.com Merck KGaA Frankfurter Str. 250 D 64293 Darmstadt Homepage: http://www.merck.de
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