[Chimera-users] normalizing attributes through point mutant models

Elaine Meng meng at cgl.ucsf.edu
Thu Jun 5 18:09:33 PDT 2014


Hello Ruben,
If you were asking how to get consistent coloring for the atomic "overlap" attribute for the different complexes:

Just make sure to use the same color for the same overlap value.  For example, if you color the first complex with yellow for 0.5 overlap and red for 1.0 overlap, make sure to color the other complexes with yellow for 0.5 overlap and red for 1.0 overlap.

You can control which color goes with which value in the Render by Attribute tool, as mentioned in the earlier reply:
> in the Render by Attribute tool: you can move the colored bars on the histogram directly with the mouse or by typing in values, change the colors of the bars, etc. as explained here:
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#colors>

... or if you use the "rangecolor" command, you specify which color goes with which value directly in the command:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rangecolor.html>

Otherwise, I don't know what you are asking.  If I haven't already answered your question, you would need to say more about which Chimera tool you are using to study these interfaces, what values you are trying to display (number of clashes? atomic overlap values?), how you are displaying them (with color? with lines?) and exactly what you mean by weighting or normalizing (are you trying to divide the values by some other values?).  Since I already described all the related features I can think of, however, there probably isn't a Chimera tool that does exactly what you wanted.

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






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