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 is probably what I am looking for.
So I will try that out.

Best

Troels Emtekær Linnet


2012/7/14 Thomas Holder <speleo3@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.vertrees@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

------------------------------------------------------------------------------
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
_______________________________________________
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net