Dear Pymolers.

Thanks for all the suggestions. :-)

I definitely think that 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.


Troels Emtekær Linnet

2012/7/14 Thomas Holder <>
indeed, the SITE records could easily be parsed and made available as
named selections.

  -> makes named selections from uniprot annotations


Nat Echols wrote, On 07/13/12 23:24:
> On Fri, Jul 13, 2012 at 2:12 PM, Jason Vertrees
> <> 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:
> For instance, trypsin (
> 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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