Dear Hussein,

Great to hear from you! (Hope things are wonderful in Claremont - it's been 
ages since I've visited.)

If you haven't built Avogadro v2, that's probably the first place to start. 
There are build instructions here:
http://wiki.openchemistry.org/Build

The next step would be to submit a small bug-fix patch, e.g., something from 
the avogadrolibs issues:
https://github.com/openchemistry/avogadrolibs/issues

A key component of the project would be to port the existing 3Dmol.js code to 
Avogadro2. I'm sure there are more components for "reach" goals, since the 
biological tracking/visualization code in Avogadro v2 is pretty much in its 
infancy. (And there's nothing saying that you need to restrict yourself to the 
3Dmol.js code, only that it exists, and I've heard comments that people like it 
better than PyMOL.)
https://github.com/3dmol/3Dmol.js/blob/master/3Dmol/glcartoon.js

Beyond that, I'd be happy to talk more as you start to put together a proposal 
draft.

Thanks and best regards,
-Geoff

---
Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: geo...@pitt.edu
twitter: @ghutchis
web: https://hutchison.chem.pitt.edu/

> On Mar 23, 2019, at 5:52 PM, Hussein Faara <faarahuss...@gmail.com> wrote:
> 
> Hello Geoffrey,
> 
> I'm Hussein, and I'm currently a sophomore at Pomona College studying
> computer science and molecular biology. Having previously taken
> biochemistry and used computational modelling programs like PyMOL to
> visualize bio-molecular structures and to predict the structural
> effects of mutations on such structures, I am very interested in
> implementing such functionality into the Avogadro suite as efficiently
> as I can. The explanatory content on the Open Chemistry site is a
> little short an was wondering if I could in any way have access to
> more information about the said project, perhaps the code suite to
> more effectively write a proposal. Thank you, and I look forward to
> hearing from you.
> 
> Sincerely,
> Hussein Faara

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