[Chimera-users] normalizing attributes through point mutant models

Elaine Meng meng at cgl.ucsf.edu
Fri May 30 15:16:16 PDT 2014


Hello Ruben,
With Find Clashes/Contacts, clashes can be shown with lines and/or by coloring the clashing atoms a single color:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash.html>

It also allows assigning the "overlap" attribute of atoms so that you can color individual atoms differently depending on the amount of overlap, using Render by Attribute.  
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#render>

It sounds like you didn't understand how to change the values-to-colors mapping in Render by Attribute. This is *not* done in the Color Key tool.  Instead it is done 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>

After you have the desired value-to-color mapping already figured out in Render by Attribute, then you might draw a color key to include in a figure.  For example, in this image, the color key is the rectangle below the structure:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/2gbp-bfactor.png>

Secondly, I don't understand what normalization you are trying to do, or why. It seems (to me) that the actual overlap values and counts of clashes would be more meaningful for comparison of the complexes.
Best wishes,
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 May 28, 2014, at 11:15 AM, Rubén Marrero Diaz De Villegas wrote:

> Hello
> I´m working with one antigen/antibody complexes and different point mutations at the interface. I can calculate and draw at the surface attributes like atomic clashes “overlap”, but what I don´t know, is how to normalize the calculation output for 2 complexes, neither render such “normalized” attributes in the models.
>  
> I have tried at Render attribute tool, the option “create corresponding color key”, introducing specific clashes boundaries and their coloring values but there is no “apply” button, such the changes doesn’t goes to the model. 
> Any help or tip?
> Thanks  in advance
> Ruben




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