Re: [ccp4bb] PDB format survey?

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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Subject: Re: PDB format survey?
From: Bernhard Rupp bernhardrupp {- at -} SBCGLOBAL {- dot -} NET
Date: 2007-08-02

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Subject: imgCIF workshops at BSR 2007
From: "Herbert J {- dot -} Bernstein" yaya {- at -} BERNSTEIN-PLUS-SONS {- dot -} COM
Date: 2007-08-02

Subject: Re: PDB format survey?
From: Kevin Cowtan cowtan {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-08-02

Does it matter what the PDB use? They will export PDB and mmCIF for us
to use, so what they use internally doesn't matter. (IIUC the EBI uses SQL).

From my perspective as a developer I am not bothered in the slightest
whether we use PDB or mmCIF, because I read everything through MMDB
which handles both. Currently I write out PDB, but I can put in a switch
trivially. Any other alternative would require a certain amount of
coding work in MMDB.

Single letter chain IDs cause me a bit of pain in buccaneer.

Kevin

Joe Krahn wrote:
> So, I am thinking about putting up a survey somewhere to get a measure
> of the user-communities interests, because RCSB and wwPDB seem
> uninterested in doing so. Maybe a group result would be more useful in
> influencing the standards. I am hoping that the wwPDB can become a
> better place for format standards instead of RCSB which keeps busy
> handling new data.
>
> In addition to questions about the PDB standard, it is probably
> important to consider mmCIF. One thing I don't like about it is that
> columns can be randomized (i.e. X, Y, and Z can be in any column), but
> the mmCIF standards people have no interest in defining a more strict
> standard that would require files to be as human readable as RCSB's
> mmCIF files.
>
> Does this sound useful, or have most people given up on having any
> influence on standards? Or, should the structural biology software
> developers get together and just make our own OpenPDB format?
>
> Joe Krahn

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: PDB format survey?
From: Bernhard Rupp bernhardrupp {- at -} SBCGLOBAL {- dot -} NET
Date: 2007-08-02

Next message:
Subject: imgCIF workshops at BSR 2007
From: "Herbert J {- dot -} Bernstein" yaya {- at -} BERNSTEIN-PLUS-SONS {- dot -} COM
Date: 2007-08-02