[Chimera-users] Color by ramachandran probability? Or molprobity overlap?

Elaine Meng meng at cgl.ucsf.edu
Thu Dec 19 15:23:37 PST 2013


Hi Oliver,
I agree it would be useful.  I wouldn't be the one doing the implementation, so it depends on how developer time is triaged, but your request has been entered into our tracking database as report #12711.  Your email address is already on the report for automatic notification of comments or changes related to the request.
<http://plato.cgl.ucsf.edu/trac/chimera/ticket/12711>

We're glad you like Chimera, and thanks for the suggestion!
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 Dec 19, 2013, at 8:13 AM, Oliver Clarke <olibclarke at gmail.com> wrote:

> Hi Elaine,
> 
> Apologies for the late response, and thank you very much for taking the time to reply. 
> 
> Yes, I could do that with some effort, but I was thinking of this more as a routine tool for checking out problematic regions of a structure either while building my own structures, or when inspecting structures in the PDB that I want to interpret - there is no good way that I am aware of at the moment to globally display Ramachandran outliers on a structure, without doing the sort of scripting you describe. 
> 
> Chimera is may favorite tool for visualizing protein structures and making figures, so it would be wonderful to have such functionality - it would also be useful when preparing validation figures, for example to show reviewers that the only geometric outliers in your structure lie in high b-factor, relatively mobile loops.
> 
> Thanks again,
> Oliver.




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