Question: molecular viz tools (eg, PyMol) and R?
11.1 years ago by
Paul Shannon • 1.1k
Paul Shannon • 1.1k wrote:
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 with hydrophobicity? With structural loops? Visual exploration of those sites 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. Thanks! - Paul
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