[Chimera-users] normalizing attributes through point mutant models

Elaine Meng meng at cgl.ucsf.edu
Thu Jun 5 16:04:50 PDT 2014


Hi Ruben,
I don't understand your wish to "normalize".  If I were comparing the different structures, I would just get the count of how many clashes (or H-bonds or whatever you are looking at) there are in each structure, perhaps for the whole interface and/or just involving the one residue that is different, and simply report those numbers. 

Maybe you want to divide by something, like number of residues or surface area of interface.  However, you didn't say what the "something" is, so I have no way of answering whether you can measure that "something" or not.  Even if you can measure it (for example, "measure buriedArea" command <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html> ) if I were trying to do something like that I would just do the 5 measurements and the 5 divisions "manually" (like with a calculator).
Best,
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 Jun 5, 2014, at 8:16 AM, Rubén Marrero Diaz De Villegas <marrerodiaz.ruben at inta.gob.ar> wrote:

> Elaine
> 
> Thanks for your opinion
> Now I understand, i was wrong about the usage of " create corresponding color key "
> Anyway, and as example, suppose I load 5 interaction complexes in chimera, the 5 complexes have the same AA sequence , differing only in one AA,  then I need to weight, or  evaluate in some way, the relevance of the point mutations in the interacting interface at each complex, and visualize and plot this calculation, Do I made such task in chimera ?? and HOW? remember, there is 5 interfaces with individual values that must be compared.
> For example, comparing the atomic clashes between interface residues ?
> 
> Thanks in advance
> 
> Ruben




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