The main technology I've seen used for interactive publications is ActiveICM (see http://www.molsoft.com/activeicm.html#aipub ). In my lab, we regularly include pymol sessions as supplementary material to help people understand our results.

-David

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?
 
Best
Troels Emtekær Linnet
PhD student
SBiNLab, Copenhagen University
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