[Chimera-users] question about surface properties in Chimera

Katherine Klymko katieklymko at gmail.com
Thu Jul 5 09:49:10 PDT 2012

Thank you for the help. I have another question: Is it possible to write a
file with a list of the amino acids on the surface, and possibly their
locations relative to the center of mass of the protein?

Thank you,


On Wed, Jul 4, 2012 at 12:53 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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.
> <
> http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#render
> >
> 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:
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/hydrophob.html>
> 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
> -----
> 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
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