[BioPython] 3D Structure?

[Catherine Letondal]

On Dec 17, 2004, at 5:43 AM, Andrew Dalke wrote:
>
>>> 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.
>
> Except that people wouldn't use that API.  To be useful, the
> OpenGL window needs to be embedable in a GUI, so that the rotating
> molecule is in a Qt or wx or other such window.  It also needs
> support for mouse interactions, so that clicks and mouseovers work.
>
> More advanced widgets would need support for displaying multiple
> molecules, or multiple conformations of a part of the structure
> as with docked poses.   It should also allow people to insert
> arbitrary graphics objects in the scene, which is useful for making
> diagrams or new types of representations.  And ideally do so
> with proper support for transparency and the ability to dump the
> structure out to Raster3D, POV-Ray or other rendering software.

Hi,

I have started to wrap (with Tkinter) a Tcl/Tk widget based on togl 
(Tcl extension for OpenGL) developed by colleagues, Pierre Tuffery 
(author of XmMol) and Bertrand Neron. Although it's not finished 
(several problems in graphics display are still not fixed), I think 
it's interesting as a building-block component that you can integrate 
as a standard Tk widget in your application. It's also designed to 
enable multiple display of either several molecules in a single widget, 
or several sub-displays showing diverse views of molecules. It's easy 
to connect with other widgets (such as a sequence, alignment, plot, ... 
widget) : this can be useful to display specific tags synchronously to 
show features.You can steer it through diverse commands (coloring, 
moving, ...) as in any Tk-based component. The project also relies on 
several user studies and prototyping workshops, made with people 
working with structures and sequences and I believe that the resulting 
tool is quite flexible.

There is no Web page at the moment, but there are some (old) 
screendumps that you can look at it here:
http://www.pasteur.fr/~letondal/biok/i3DMol.html
(where you can see how it interacts with an alignment widget and a plot 
widget).

In fact, the project is a little bit stalled, so, and I have just 
discussed with the authors about it, we would be glad if any of you 
would like to participate to the development.

--
Catherine Letondal -- Institut Pasteur
www.pasteur.fr/~letondal