The main technology I've seen used for interactive publications is ActiveICM (see ). In my lab, we regularly include pymol sessions as supplementary material to help people understand our results.


On Friday, July 13, 2012 at 6:41 AM, Troels Emtekær Linnet wrote:

Dear PyMolers.
Reading crystallographic papers, and feeling the
need for seing a papers annotation and explanation of important residues,
I often have pymol at my hand.
fetching the protein, and typing in commands to see the mentioned residues.
That is time-consuming, but okay.
Inspired by John Amraph's need for a "preset.lig​and_cartoo​n", when loadning
a paper, I would wish there were a: "preset.as_article" or a "fetch 1SVN, as_article".
Simply a pymol script file that fetch the protein, shows it as cartoon, and selecting/labelling/showing the
mentioned important residues in the article. Or the catalytic triad, the substrate channels... etc.
You get the point. :-)
So, does anyone know there already exist such a databank/annotation server?
If it exist, could one make a script that can fetch and convert these annotations to a pymol script?
Or if doesnt exist, would it be a interesting project to pursue?
Troels Emtekær Linnet
PhD student
SBiNLab, Copenhagen University
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