Print

Print


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
*******************************************************