Dear Pymolers.
Thanks for all the suggestions. :-)
I definitely think that http://jolecule.appspot.com can become handy for a
teaching situation
or sending a colleague a question to a protein. Thanks!
And I am all in for interactive publications, which I hope could use one
day.
The Uniprot_features <http://pymolwiki.org/index.php/Uniprot_features> is
probably what I am looking for.
So I will try that out.
Best
Troels Emtekær Linnet
2012/7/14 Thomas Holder <spel...@users.sourceforge.net>
> indeed, the SITE records could easily be parsed and made available as
> named selections.
>
> Similar: http://pymolwiki.org/index.php/Uniprot_features
> -> makes named selections from uniprot annotations
>
> Cheers,
> Thomas
>
> Nat Echols wrote, On 07/13/12 23:24:
> > On Fri, Jul 13, 2012 at 2:12 PM, Jason Vertrees
> > <jason.vertr...@schrodinger.com> wrote:
> >> It would be nice if publishers required a common CSV format for
> >> specifying contacts and annotations. Then we could easily pull the
> >> data from reliable resources. But, alas, this doesn't exist.
> >
> > One possible (albeit incomplete) way to do this is with the SITE
> > records in PDB files:
> >
> > http://www.wwpdb.org/procedure.html#toc_10
> >
> > For instance, trypsin (
> http://www.rcsb.org/pdb/files/1SGT.pdb?headerOnly=YES):
> >
> > SITE 1 CAT 3 HIS A 57 ASP A 102 SER A 195
> > SITE 1 AC1 6 ASP A 165 ALA A 177A GLU A 180 GLU A 230
> > SITE 2 AC1 6 HOH A 259 HOH A 261
> >
> > Obviously this still requires that the authors actually perform the
> > annotation. It's a poor substitute for having (for instance) entire
> > PyMOL sessions accompanying a PDB deposition, but I've learned to keep
> > my expectations low.
> >
> > -Nat
>
> --
> Thomas Holder
> MPI for Developmental Biology
> Spemannstr. 35
> D-72076 Tübingen
>
>
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