[Chimera-users] Upload color scheme

[Cornelius Hunter]

Elaine:

Thank you, this looks like it will do the job nicely. I did not see this
helpful documentation because I was looking in the User's Guide->Basic
Functions->Coloring:

http://www.rbvi.ucsf.edu/chimera/current/docs/UsersGuide/framecore.html

Thanks very much again, I look forward to trying this out.

--Cornelius



On Fri, May 10, 2019 at 4:09 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Cornelius,
> If you have a numerical value for each residue and you would like
> flexibility with coloring by those values, the way is to create a residue
> attribute assignment file.  Reading it in just assigns the values, after
> which you can explore different colormappings for those values.
>
> Attribute assignment files are relatively simple text files described
> here, with examples:
> <
> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defineattrib.html#attrfile
> >
> The first example file is a per-residue attribute, specified by residue
> number in the structure.
>
> Opening your structure and then reading in the attribute file with Define
> Attribute (in menu under Tools… Structure Analysis) or command “defattr”
> assigns the values:
> <
> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defineattrib.html
> >
>
> Then you can try different colormappings to those values with the Render
> by Attribute GUI (in menu under Tools… Depiction or Structure Analysis) or
> the “rangecolor” command.  You can have any number of colors spaced however
> you like along the value range.
> <
> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#render
> >
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rangecolor.html>
>
> It is similar to coloring by B-factor except you can have any number of
> your own custom attributes for the same structure, and they can have more
> significant digits than would fit in the PDB B-factor column.
>
> See also tutorials…
> Attributes
> <
> http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/attributes.html
> >
> Bfactor coloring
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/bfactor.html>
> Coloring by surface properties
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.html>
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> > On May 10, 2019, at 9:38 AM, Cornelius Hunter <chunter at jessup.edu>
> wrote:
> >
> > I am looking for a 3D protein viewer that allows me to visualize the
> protein tertiary structure using my own color assignments, for each residue
> (or alpha carbon). In other words I would upload a file, with a value for
> each residue, which would drive the color assignments. Thx
>


-- 
*Cornelius Hunter*
   *Adjunct Professor, Natural Sciences*
WILLIAM JESSUP UNIVERSITY - Rocklin Campus
2121 University Avenue, Rocklin, CA 95765
P (530) 677-2046 | chunter at jessup.edu
jessup.edu
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