Dear CCP4ers,
Kim Henrick from EBI sent me pointers to
http://ligand-expo.rcsb.org/ld-search.html
and to
http://www.ebi.ac.uk/msd-srv/msdchem/cgi-bin/cgi.pl
for looking up reference dictionaries. Especially, the first link turns
out to be a gorgeous site for getting refrence dictionaries! This is
exactly what I was looking for, and, in my opinion, both sites should be
prominently linked from www.pdd.org/www.wwpdb.org.
Many thanks to Randy Read, Miri Hirshberg and Kim Henrick for your fast
help!
Best regards,
Dirk.
Am 11.02.10 11:19, schrieb Dirk Kostrewa:
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
*******************************************************
