Once again Thomas Holder have done a very nice work, and made a solution.
Check it out here:
http://www.pymolwiki.org/index.php/Select_sites
fetch 1sgt, async=0import select_sites
select_sites
It works really brilliant.
Best
Troels Emtekær Linnet
2012/7/14 Troels Emtekær Linnet <tlin...@gmail.com>
> 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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