[Chimera-users] Surface electrostatic and hydrophobicity.

[Elaine Meng]

Hi Sumitro,
(1) Sorry no, Chimera does not have atomic hydrophobicities built in, and there is nothing like a "hydrophobic potential" that uses atomic hydrophobicities and the distances from the atoms.  If you have a list of atomic hydrophobicities and know how you want to map those values to specified atoms in Chimera, you could create and apply an "attribute definition" file to assign the atomic values. 
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defineattrib.html>
Then you could use Render by Attribute to color by the atomic values, but it would just color the surface from each atom rather than smearing it out in space like a potential.  Also, it would be some work for you to create the attribute definition file.  

One possibly crazy idea of mine is to use Add Charge and use atomic charges as a proxy for hydrophobicity: in Render by Attribute, define a color mapping to atomic charge that shows larger-magnitude negative and positive values with some "polar" color, and near-zero values with some "hydrophobic" color.  I don't know how well that would work.

(2) The Coulombic equation is different and the calculation much simpler than Poisson-Boltzmann continuum electrostatics calculations (such as done by DelPhi, Grasp, APBS, and UHBD), and the results will not be exactly the same.  How the Coulombic tool works is described in the User's Guide:
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/coulombic.html>
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/coulombic.html#hydrogens>

For *quantitative calculations*, Coulombic is not as good.  However, for *visualization*, in practice we have found that the surface coloring turns out much the same.  There is an informal comparison here:
<http://tinyurl.com/mzopva>

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 Jan 28, 2011, at 4:40 AM, Sumitro Harjanto wrote:

> Hi elaine,
> 
> I've a few questions to ask about colouring surface by electrostatic potential and hydrophobicity:
> 
> 1. I understand that I can use render by attribute to show surface hydrophobicity. But because it's a residue attribute, any surface of the same residue will be getting the same colour. Is there a way to calculate the surface hydrophobicity based on atoms in the vicinity instead of simply using the residue hydrophobicity values?
> 
> 2. Because I have problem installing delphi, I have resorted to using the coulomb surface colouring tool. How different is this from the procedure of adding hydrogen, adding charge, then render by attribute ? Will I expect to see the same result ?
> 
> Thanks elaine!
> 
> Cheers,
> Sumitro
>