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CCP4BB  February 2010

CCP4BB February 2010

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Subject:

Re: PDB 3.2 Nomenclature

From:

Miri Hirshberg <[log in to unmask]>

Reply-To:

Miri Hirshberg <[log in to unmask]>

Date:

Thu, 11 Feb 2010 10:04:55 +0000

Content-Type:

TEXT/PLAIN

Parts/Attachments:

Parts/Attachments

TEXT/PLAIN (143 lines)

Thurs. Feb. 11th 2010
EBI

Dear Dirk,

I see your point regarding the documentations, PDB is vast..
What exactly would you like to have?

Miri

On Thu, 11 Feb 2010, Dirk Kostrewa wrote:

> Hello Miri,
>
> yes, but if you look into these documents, they don't contain a good 
> dictionary of the usual compounds. They either have the broken link that I've 
> mentioned or point to the ftp-site with its cryptic collection.
>
> Anyway, thanks for the pointer.
>
> Best regards,
>
> Dirk.
>
> Am 11.02.10 10:36, schrieb Miri Hirshberg:
>> Thurs., feb. 11th 2010
>> EBI
>> 
>> Hello,
>> 
>> to add to Randy Read's note, the following URL has
>> 
>> http://www.wwpdb.org/docs.html
>> 
>> has this documment and others in PDF or HTML
>> 
>> Miri
>> 
>> On Thu, 11 Feb 2010, Randy Read wrote:
>> 
>>> Dear Dirk,
>>> 
>>> By coincidence, I was talking on Tuesday to Jawahar Swaminathan (at PDBe 
>>> at the EBI), mentioning that I'd had trouble tracking down the 
>>> documentation, and he forwarded me a link:
>>> 
>>> http://www.wwpdb.org/documentation/format32/v3.2.html
>>> 
>>> Hopefully that has the information you need.
>>> 
>>> Regards,
>>> 
>>> Randy
>>> 
>>> On 11 Feb 2010, at 08:55, Dirk Kostrewa wrote:
>>> 
>>>> Dear CCP4ers,
>>>> 
>>>> I'm desperately trying to dig out a good documentation of the new PDB 3.2 
>>>> nomenclature on www.wwpdb.org, but find myself running in circles. There 
>>>> is even a broken link to the nomenclature file 
>>>> http://remediation.wwpdb.org/downloads/Components-rel-alt.cif. The other 
>>>> link, ftp://ftp.wwpdb.org/pub/pdb/data/monomers, is a cryptic collection 
>>>> of compounds.
>>>> Why isn't there a document for PDB 3.2 that covers the main dictionaries 
>>>> for amino acids, nucleic acids, sugars, water and so on (maybe with a 
>>>> useful link to more exotic compounds) like for the old PDB 2.3?
>>>> Currently, I have to rely on the "remediator" program from the Richardson 
>>>> lab for that, without even knowing whether it is always correct. How 
>>>> could I possibly write a program that reads/writes PDB 3.2 files 
>>>> correctly?
>>>> 
>>>> I would be very grateful for any useful document.
>>>> 
>>>> 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:    [log in to unmask]
>>>> WWW:    www.genzentrum.lmu.de
>>>> *******************************************************
>>> 
>>> ------
>>> Randy J. Read
>>> Department of Haematology, University of Cambridge
>>> Cambridge Institute for Medical Research      Tel: + 44 1223 336500
>>> Wellcome Trust/MRC Building                   Fax: + 44 1223 336827
>>> Hills Road                                    E-mail: [log in to unmask]
>>> Cambridge CB2 0XY, U.K.                       www-structmed.cimr.cam.ac.uk
>>> 
>> 
>> Thurs., Feb. 11th 2010
>> EBI
>> 
>> ------------------------------------
>> Dr Miri Hirshberg
>> European Bioinformatics Institute UK
>> PDBe - EBI -EMBL
>> http://www.ebi.ac.uk/pdbe
>> 
>> Phone: +44 (0) 1223 492647
>> FAX:   +44 (0) 1223 494468
>> ------------------------------------
>
> -- 
>
> *******************************************************
> 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:	[log in to unmask]
> WWW:	www.genzentrum.lmu.de
> *******************************************************
>

Thurs., Feb. 11th 2010
EBI

------------------------------------
Dr Miri Hirshberg
European Bioinformatics Institute UK
PDBe - EBI -EMBL
http://www.ebi.ac.uk/pdbe

Phone: +44 (0) 1223 492647
FAX:   +44 (0) 1223 494468
------------------------------------

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