[Chimera-users] pH-dependent surface potential

Elaine Meng meng at cgl.ucsf.edu
Sat Oct 15 09:30:11 PDT 2011

Hi Dieter,
Yes, if you didn't already add hydrogens, Chimera will use reasonable protonation of functional groups at pH 7, without considering how the local environment might shift pKa (except for histidine: default in Coulombic Surface Coloring is to use the local environment to determine which nitrogen of the sidechain, or possibly both, should be protonated, but you can specify them individually). 

However, you can control the protonation states of not only histidine but other ionizable residues by adding hydrogens before using Coulombic Surface Coloring.  Chimera wouldn't figure it out for you, but for the AddH tool you can specify individually how to protonate the ionizable sidechains, either by using special residue names or interactively, see the docs:

To actually predict pKas and thus assign states at a particular pH, you would need to go outside of Chimera.  There are some useful web servers, for example:



One issue in Chimera is that the molecular surface with hydrogens is "bumpier" -- you might want to use the Coulombic options to create a grid of the potential, then use that grid data to color the molecular surface of the structure without hydrogens.

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

On Oct 15, 2011, at 1:45 AM, Dieter Blaas wrote:

> Hi,
>      Is there an (easy) way of displaying the surface potential at 
> different pH values within Chimera? The Chimera-contained Coulombic 
> Surface Colouring does not appear to take into consideration the 
> pH-dependent protonation state (as far as I understand it assumes pH 7).
> Thanks a lot for hints,  Dieter
> -- 
> ------------------------------------------------------------------------
> Dieter Blaas,
> Max F. Perutz Laboratories.
> Medical University of Vienna,
> Inst. Med. Biochem., Vienna Biocenter (VBC),
> Dr. Bohr Gasse 9/3,
> A-1030 Vienna, Austria,
> Tel: 0043 1 4277 61630,
> Fax: 0043 1 4277 9616,
> e-mail: dieter.blaas at meduniwien.ac.at
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