As the constant flow of emails suggest, you are very hard at work with this application. And I am eagerly anticipating your results, re custom labels for the atoms.
I know temporary solution, but it will not save these custom labels in file. If it satisfies you, I can try to implement it
I look forward to utilizing Avogadro for social research purposes, and think that it can be a unique and powerful tool in this field. I
Out of curiosity: how Avogadro can help you in social research? It only visualizes molecules, not people 
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Regards,
Konstantin
I know temporary solution, but it will not save these custom labels in file. If it satisfies you, I can try to implement it
When you say that it will not save the labels, does this mean that after the program quits changes are not saved?
Yes. And I see it’s not you want
Out of curiosity: how Avogadro can help you in social research? It only visualizes molecules, not people
I treat the atoms as people or things, labelled accordingly. Relationships and association are illustrated by the bonds. See MacFamilyTree - Modern genealogy for your Mac as an example of a 3D chart, however, I like the look and dynamics of Avogadro a lot better. macfamilytree is far too complex.
Are you shure you need 3D diagram with OpenGL rendering? Maybe you need simpler solution? You can try to search it in SourceForge or somewhere else
Anyway, I don’t think Avogadro in its current state will be very useful for your purpose. I believe it’ll be more productive to develop separate application, probably with use of Avogadro’s GLWidget for visualization. Another way is to create additional set of “sociological” plugins/rendering engines for Avogadro, and throw away molecule-related ones. But it doesn’t lay in field of our interest
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Regards,
Konstantin