[BioC] molecular viz tools (eg, PyMol) and R?
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
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
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
work -- but if anyone has any advice, I'd love to hear it.
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