[chimera-dev] Hydrophobicity

Elaine Meng meng at cgl.ucsf.edu
Thu Sep 18 09:21:27 PDT 2008

On Sep 17, 2008, at 10:14 PM, Leo O'Young wrote:
> I am new to the list, I am wondering if it is possible to increase  
> the geometry
> of the Hydrophobicity-Surface models.
> Thanks,
> Leo

Hi Leo,
The "hydrophobicity" in the preset is just a coloring scheme, so I  
will set that aside and discuss molecular surfaces.

I am not sure what you mean by "increase the geometry."  There are  
several ways you can adjust molecular surfaces in Chimera:  change  
vertex density, probe radius, and also the radii of the underlying  
atoms.  It is a molecular surface by the Richards definition, also  
known as the solvent-excluded surface, made of probe contact and re- 
entrant patches; it shows the VDW surface of the structure except with  
crevices smoothed.  Currently Chimera does not show the solvent- 
accessible surface, which is where the probe center goes.

If you mean you want to make the surface "bigger" to enclose a greater  
volume, that can be done by increasing the VDW radii of the atoms, and  
to a lesser extent, increasing the probe radius, which will smooth the  
crevices more.  One way to increase VDW radii is with a command; this  
would increase all radii by 0.7 A, for example:

vdwdefine +0.7

(the command ~vdwdefine changes the radii back to defaults).

To change probe radius or other parameters of an existing molecular  
- Ctrl-click the surface to select it
- open the Selection Inspector (click the greenish button on the lower  
right corner of the Chimera window or choose Actions... Inspect from  
the menu)
- in that dialog, Inspect "MSMS surface", and then edit the various  
parameters as desired

You can also set preferences to use different parameters for surfaces  
created in the future, so you don't have to change each one after you  
create it.  To do that, choose Favorites... Preferences, go to the New  
Surfaces category, change parameters as desired and click Save.  That  
only pertains to surface parameters, not VDW radii of atoms, however.

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

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