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

Thomas Girke 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  
> 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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Thomas Girke
Assistant Professor of Bioinformatics
Director, IIGB Bioinformatic Facility
Center for Plant Cell Biology (CEPCEB)
Institute for Integrative Genome Biology (IIGB)
Department of Botany and Plant Sciences
1008 Noel T. Keen Hall
University of California
Riverside, CA 92521

E-mail: thomas.girke at ucr.edu
Website: http://faculty.ucr.edu/~tgirke
Ph: 951-827-2469
Fax: 951-827-4437

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