Dear Randy,
I've found this link already, but it is not very useful, because it only
generally describes the format. What is missing, is a good actual
dictionary of the usual compounds (amino acids, nucleic acids, and so
on). In the coordinate section, it only provides a link to the ftp-site
with its cryptic collection of compounds.
Many thanks, aynway!
Best regards,
Dirk.
Am 11.02.10 10:27, schrieb Randy Read:
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
--
*******************************************************
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
*******************************************************
