Re: [ccp4bb] Official PDB Nomenclature?

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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Subject: Re: precipitation of the protein in crystallisation solution
From: Enrico Stura estura {- at -} CEA {- dot -} FR
Date: 2009-06-03

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Subject: Re: Official PDB Nomenclature?
From: Dirk Kostrewa kostrewa {- at -} LMB {- dot -} UNI-MUENCHEN {- dot -} DE
Date: 2009-06-03

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: kostrewa@lmb.uni-muenchen.de
>> >
>> *******************************************************

*******************************************************
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: kostrewa@lmb.uni-muenchen.de
*******************************************************

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: precipitation of the protein in crystallisation solution
From: Enrico Stura estura {- at -} CEA {- dot -} FR
Date: 2009-06-03

Next message:
Subject: Postdoctoral Positions in Ion Channel Structure at UCSF
From: Dan Minor daniel {- dot -} minor {- at -} UCSF {- dot -} EDU
Date: 2009-06-03