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
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------
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
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