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@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/defin...
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/defin...
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...
<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@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@jessup.edu jessup.edu