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.ligand_cartoon", 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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