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
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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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