If you want dictionary, atom naming and everything else about new
compound names you can copy all "monomers" (in our definition) from:
ftp://ftp.ebi.ac.uk/pub/databases/rcsb/pdb-remediated/data/monomers/components.cif.gz
It has all compounds used in pdb with "idealised" coordinates,
compound names with their some characteristics, new atom names as well
as alternative atom names.
Good luck.
Regards
Garib
On 11 Feb 2010, at 10:19, Dirk Kostrewa wrote:
Dear Miri,
thanks a lot for looking after this! I would like to have the actual
reference dictionaries for the most frequent and important compounds
in PDB files: amino acids, desoxy-ribonucleotides and ribonucleotides.
If there is anything special in the convention about water, metal
ions, halides, sulfate, phosphate and alike, I would also like to
have quick access to their dictionaries. Access to dictionaries of
other more or less frequently used compounds, like sugars, co-
factors, and so on, would also be much appreciated.
I can imagine, that a single document describing all possible
compounds would be simply too big. Personally, I think, a web-site
containing links to the dictionaries of amino acids, nucleic acids,
sugars, water, ions, co-factors and so on would be really helpful.
Such a site could be subdivided into categories, alphabetically, or
any other order that would help the users to get quick access to the
required information.
Best regards,
Dirk.
Am 11.02.10 11:04, schrieb Miri Hirshberg:
Thurs. Feb. 11th 2010
EBI
Dear Dirk,
I see your point regarding the documentations, PDB is vast..
What exactly would you like to have?
Miri
On Thu, 11 Feb 2010, Dirk Kostrewa wrote:
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: [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
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: [email protected]
WWW: www.genzentrum.lmu.de
*******************************************************
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: [email protected]
WWW: www.genzentrum.lmu.de
*******************************************************
