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: [email protected] > 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: [email protected] Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
