[BioC] molecular viz tools (eg, PyMol) and R?
thomas.girke at ucr.edu
Sat Jul 26 18:40:08 CEST 2008
Have you looked into Bio3D in R from Grant et al
(Bioinformatics 22, 2695-2696). The project URL is:
I am not sure if it provides the exact utilities you are
looking for but it may be worth to take a look.
On Sat, Jul 26, 2008 at 09:21:26AM -0700, Paul Shannon 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
> 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
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
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E-mail: thomas.girke at ucr.edu
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