Dear Robbie,
thanks for the pointer, but I was more looking for a document with the
nomenclature for common residues. For instance, I want to know, how a
desoxy-adenosine in a nucleic acid must be correctly named. On this
web-site, I can only search for individual components, like adenine.
So, I'm still looking for a PDB nomenclature document ...
Regards,
Dirk.
Am 03.06.2009 um 10:54 schrieb R.P. Joosten:
Dear Dirk,
Ligand expo has the correct atom names and connectivity for all
existing compounds in the PDB. For instance http://ligand-expo.rcsb.org/reports/A/ACY/index.html
Please make sure that you get the terminal atoms correct. There are
quite a few PDB files that have/had terminal nucleic acid atoms with
the wrong name.
Regards,
Robbie Joosten
Dirk Kostrewa wrote:
Dear CCP4ers,
we want to deposit some structures containing amino acids and
nucleic acids, but apparently the nomenclature for nucleic acids
has changed. In former times (PDB version 2.x), there was a
complete description for the PDB nomenclature, but I can't find it
anymore for the current PDB version 3.2 (http://www.wwpdb.org/docs.html
)! When I browse through slightly older description, there is only
a hint that the IUPAC nomenclature was adapted, with a broken link.
Is there still an official PDB nomenclature that I can use to get
our structures PDB-conform? I find it strange, that there seems to
be no easily accessible PDB nomenclature description anymore ...
Best regards,
Dirk.
*******************************************************
Dirk Kostrewa
Gene Center, A 5.07
Ludwig-Maximilians-University
Feodor-Lynen-Str. 25
81377 Munich
Germany
Phone: +49-89-2180-76845
Fax: +49-89-2180-76999
E-mail: [email protected] <mailto:[email protected]
>
*******************************************************
*******************************************************
Dirk Kostrewa
Gene Center, A 5.07
Ludwig-Maximilians-University
Feodor-Lynen-Str. 25
81377 Munich
Germany
Phone: +49-89-2180-76845
Fax: +49-89-2180-76999
E-mail: [email protected]
*******************************************************
