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: [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
> *******************************************************
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