[Chimera-users] Hydrophobicity surface

[Elaine Meng]

On Jun 10, 2010, at 5:41 AM, Beale, John wrote:

> I am creating a hydrophobicity surface for a protein using the “Presets -> Hydrophobicity surface”  commands. I would like to know what the colors on the surface are telling me. I see a couple of shades of blue, white, and pink to orange. What do these colors mean?

Hi John,
The presets are described here:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/menu.html#menupresets>

"The hydrophobicity surface preset shows amino acid hydrophobicity in the Kyte-Doolittle scale with colors ranging from dodger blue for the most hydrophilic to white at 0.0 to to orange red for the most hydrophobic (different color-codings can be applied with rangecolor or Render by Attribute). Surfaces of nonpeptides will be colored to match the underlying atoms instead."

I provide the link above because the text is hyperlinked, so you can look up more information about the "Kyte-Doolittle scale" and the command "rangecolor" and the tool "Render by Attribute."

For example, if you wanted to change how the amino acid hydrophobicity values are mapped to color, you could start Render by Attribute (in menu under Tools... Depiction).   In the resulting dialog, you can change to Attributes of "residues" (instead of "atoms") and then choose the Attribute: kdHydrophobicity.  Then it will show a histogram of the values and colored vertical bars.  You can move the vertical bars and change their colors, then Apply the new color-mapping. 

You can see there are other attributes available for atoms (for example, bfactor) and residues, and you can color the atoms and ribbons as well as surfaces.  You can even show the values with sphere sizes or "worms" instead of with color. Another way to see the instructions for Render by Attribute is to click the Help button on that dialog.  Finally, this tool is also used in several of the tutorials, e.g.

<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/bfactor.html>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/attributes.html>

This is more information than just what you asked, but I thought you might be interested in exploring these features!  Best,
Elaine
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Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco