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
*******************************************************
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