[BioPython] 3D Structure?

[Kael Fischer]

Andreas:

Although not part of Biopython, UCSF Chimera is another python/open GL 
based structure analysis application.  I use it to prepare graphics for my 
lectures, do comparative modeling, surface analysis, etc.  It is supposed 
to be extensible, but I haven't explored that side of it.

Citation and link:
Pettersen, E.F., Goddard, T.D., Huang, C.C., Couch, G.S., Greenblatt, D.M., 
Meng, E.C., and Ferrin, T.E. "UCSF Chimera - A Visualization System for 
Exploratory Research and Analysis." J. Comput. Chem. 25:1605-1612 (2004).

http://www.cgl.ucsf.edu/chimera

Best,
Kael



At 02:51 AM 12/16/2004, Andreas Klostermann wrote:
>Hi,
>
>I just started browsing around what you can do with Biopython, for some
>educational interest. I'd like to try and implement an Open GL Viewer
>for molecules in Python. In my wild days (before studying veterinary
>medicine) I acquired a solid grasp of Open Gl. In case you wonder, if
>Python is fast enough for this task. It is. Or better: it's not, but
>Open Gl does all the work with hardware acceleration, circumventing the
>speed draw-back of python.
>
>First task would be to obtain the structure of the molecule by linking
>3D coordinates together. I browsed in the biopython documentation, but I
>did not really get a clue. I suspected the neccessary functionality in
>the PDB module, but could not find a way on how to get to 3D coordinates
>out of a pdb file or whatever data object is neccessary for that.
>
>The widget would then be used something like this, in fictional code
>without caring for module importing / referencing.
>
> >>> model = model_from_data(something)
> >>> window = gl_window(model)
> >>> window.show()
>
>A window would popup now, with a slowly rotating molecule in it. One
>tricky part will be to open a window on different platforms, but that's
>pretty simple. At first, pygame will be enough, since it runs on Linux,
>Windows and Mac, but that's a bad dependency (in my opinion). The module
>could check for availability of pyGTK, win32 or wxPython bindings and
>use them. The core of the open gl representation would not care a bit
>about the underlying windowing API.
>
>Of course that's all future for now. Even more futuristic would be to
>use the same core as a displaying widget in python-driven gui programs.
>
>It would be nice to receive some suggestions on this proposal.
>
>best regards,
>Andreas Klostermann
>
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