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

Elaine Meng meng at cgl.ucsf.edu
Wed Dec 11 10:55:57 PST 2013


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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