[BioC] molecular viz tools (eg, PyMol) and R?

Paul Shannon pshannon at systemsbiology.org
Sat Jul 26 18:21:26 CEST 2008

I have lots of phosphorylation site data, obtained from mass  
spectrometry, which I manage and explore in R.
As you'd expect, R has been very handy for finding patterns for these  
phospho-sites with respect
to their primary sequence and secondary structure predictions. Many  
bioc packages have been helpful
along the way.

Now I want to explore for patterns in the 3D structure surrounding  
these phosphorylation sites.
Do phospho-sites correlate well with surface accessibility?  Inversely  
hydrophobicity?  With structural loops?  Visual exploration of those  
in 3D renderings of their proteins pdb models seems like a good place  
to start.

In pursuit of that, I have dabbled with PyMol, DeepView, Chimera, VMD,  
and Cn3D, all of which -- along
with other similar tools -- have lots to offer. But so far as I can  
tell, none have any connection
to R.

Is there any 3D-molecular-vizualization companion to R, similar in  
spirit to rggobi or Rgraphviz?
Commands like these would be very nice:

    1) load (<pdb file>)
    2) select (<list of residues>)
    3) colorResiduesByProperty (<accessibility|hydrophobicity|..>)

I suspect that the demand for something like this is too small to  
justify the
work -- but if anyone has any advice,  I'd love to hear it.


  - Paul

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