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

Oliver Clarke olibclarke at gmail.com
Thu Dec 19 08:13:37 PST 2013

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,
On Dec 11, 2013, at 1:55 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Oliver,
> There is no automatic way (without doing some of your own processing), but if you can calculate the values, it is fairly easy to assign them as attributes.  Then you can use the Chimera "Render by Attribute" tool or "rangecolor" command to map the values to colors on the structure.
> Custom attributes are assigned by reading in an "attribute assignment file," which is basically a tab-separated columns text file with some control lines at the top. The format is described here, and several example files are provided:
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defineattrib.html#attrfile>
> Amino acid residue phi and psi angles are already attributes, but there is no automatic assessment of how well they agree with a Ramachandran map in Chimera other than actually displaying the map with the values plotted (which can be done via the Model Panel, as you saw).  Your processing would need to compare the phi and psi values with Ramachandran plot contours and distill that into some value that could be assigned as a residue attribute (analogously you could take the molprobity output values and assign them as atom attributes), then generate a corresponding attribute assignment file.  After reading your custom attribute in, you could use Chimera's existing coloring-by-attribute features, as mentioned above.
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#render>
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rangecolor.html>
> I hope this helps,
> 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 10, 2013, at 6:34 PM, Oliver Clarke wrote:
>> Hi all,
>> Quick question, just wondering if there is any way to color a structure by Ramachandran probability? Or by steric overlap scores for each atom as generated by mol probity? 
>> Either of these would be very handy as a way of getting a quick graphical overview of trouble spots in a structure. It seems like Chimera “knows about” Ramachandran plot data, (as one can generate such plots from the model panel) but I can’t find any convenient way to display this data on the structure.
>> Many thanks,
>> Oliver.

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