[Chimera-users] question about surface properties in Chimera

Elaine Meng meng at cgl.ucsf.edu
Wed Jul 4 09:53:34 PDT 2012

Hi Katie,
The hydrophobicity coloring in the presets menu is simply using the Kyte-Doolittle amino acid hydrophobicity values.  That is, all the surface patches belonging to a given amino acid residue type will have the same color, and the colors range from blue for the most hydrophilic through white to orange-red for the most hydrophobic.

If you open Render By Attribute (under Tools... Structure Analysis) and set it to show the attribute of "residues" named "kdHydrophobicity" you can apply a different coloring scheme to these same values.  Or, if you want, you can write out a file that lists the residues in the protein and the associated values (in that tool's menu, use File... Save Attributes).  That will include all the residues, though, not just the ones on the surface.

However, as mentioned, it is merely a lookup based on the residue type.  There is a table of Kyte-Doolittle hydrophobicity values here, and instructions for using different scales of amino acid hydrophobicity, if you would like:

We encourage Chimera questions to be sent to chimera-users at cgl.ucsf.edu (Cc'd) unless the message includes private data. 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 Jul 4, 2012, at 7:40 AM, Katherine Klymko wrote:

> Dear Dr. Meng,
> Hello--I am a theoretical chemistry student at Columbia University and I am interested in the hydrophobicity maps of proteins that Chimera generates: I know that this can be used to visualize the hydrophobicity of the surface, but does it also generate a file that I can use that lists the positions of the surface atoms or amino acids with their hydrophobic value? I am interested in quantitatively comparing the hydrophobic surface organization in a large number of proteins.
> I apologize if you are the wrong person to ask but when searching for solutions on line, you seemed to be the person that a lot of people went to for help. 
> Thank you,
> Katie Klymko

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