[Chimera-users] Calculation of Hydrophobicity

[Elaine Meng]

Hi Magnus,
Coulombic Surface Coloring (under Tools... Surface/Binding Analysis) calculates Coulombic electrostatic potential, and besides coloring a surface, includes a "Compute grid" option to create a map of the values.  When the grid is created, the Volume Viewer tool automatically appears showing a histogram of its values.  Volume Viewer can be used to save the map to a file (using its File menu) or do other things to it, such as displaying isopotential contour surfaces.
<http://plato.cgl.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/coulombic.html>
<http://plato.cgl.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/coulombic.html#volume>

Chimera doesn't do Poisson-Boltzmann calculations, but can read in electrostatic potential maps from other programs such as DelPhi, APBS, and UHBD.

The hydrophobicity coloring (for example, Presets.... Interactive 3) in Chimera only uses a lookup table of amino acid hydrophobicities. It does not do a distance-dependent "potential" calculation such as available in some other programs.  Chimera uses Kyte-Doolittle hydrophobicity values by default, but you can read in and use other amino acid hydrophobicity scales.
<http://plato.cgl.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/coulombic.html#volume>
<http://plato.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/hydrophob.html>

You can write out "attribute" values such as these for your structure using "File... Save Attributes" in the "Render by Attribute" tool (under Tools... Depiction), but in this case it would just be using the lookup value for each residue rather than computing something new.

Some other programs that may be interesting for hydrophobicity calculations:
- Platinum web server  <http://model.nmr.ru/platinum/>
- HINT (commercial)  <http://www.edusoft-lc.com/hint/>

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 Aug 16, 2011, at 3:46 PM, Magnus Andersson wrote:

> Hi,
> 
> I'm a new user to Chimera and found it very useful really fast.
> 
> I have a question however, is possible to make a calculation of the hydrophobicity of a surface or the electrostatic potential, not only show it visually?
> 
> Best regards
> Magnus