Thurs. Feb. 11th 2010
EBI
Dear Dirk
I also put to the PIs your suggestion of web-site-service, will keep you
and the rest of the community update.
Miri
On Thu, 11 Feb 2010, Dirk Kostrewa wrote:
> 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: [log in to unmask]
>>>>>>> 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: [log in to unmask]
>>>>>> 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: [log in to unmask]
>>>> 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: [log in to unmask]
> 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
------------------------------------
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