Looks like the PDB format will be changing to support larger molecules. I think
this is a good thing, although we should modify the PDB code for the new PDBx.
-Geoff
Begin forwarded message:
> Dear Geoffrey,
>
> During the past three years we have requested comments from PDB developers
> and users on how best to address limitations
> in the current PDB format representing large structures. During this period,
> a variety of options were explored including a wwPDB proposal for a new
> simplified format. Available alternatives were reviewed at a September 2011
> workshop at the EBI, where a group of X-ray and NMR software developers
> strongly recommended that PDB use the existing PDBx/mmCIF format because this
> format addresses all of the technical limitations of the current PDB format
> and software tools and support are already available.
>
> As a result of this workshop, the wwPDB convened a Working Group for
> PDBx/mmCIF Data Deposition (http://wwpdb.org/workshop/wgroup.html), chaired
> initially by Oliver Smart and presently by Paul Adams, that includes
> representatives from the major X-ray structure-determination packages. To
> ease the transition from PDB to PDBx/mmCIF, the Working Group has made
> recommendations about the essential extensions required for large structures,
> including:
>
> • Atom serial numbers will run from 1 to the number of deposited atoms
> (with no field-width restrictions);
> • Chain identifiers of up to 4 characters will be allowed;
> • Cartesian coordinates will have a field width as large as required and
> maintain 3 decimal places precision;
> • Isotropic B-factors and occupancies will have 3 decimal places precision.
>
> A recent wwDPB announcement (http://wwpdb.org/news/news_2013.html) provides
> details of the transition plan for how wwPDB will accept and release large
> structures in single PDBx/mmCIF data files, following the recommendations of
> the working group. In a nutshell, until 2014, intact large structure files
> will be released in a special location in the ftp archive ( USA:
> ftp://ftp.wwpdb.org/pub/pdb/data/large_structures, Europe:
> ftp://ftp.ebi.ac.uk/pub/databases/pdb/data/large_structures, and Japan:
> ftp://ftp.pdbj.org/pub/pdb/data/large_structures), while the “split” entries
> will continue to be released as before (so as not to break any
> PDB-archive-processing pipelines). In 2014, however, these large entries
> will begin to appear in the standard directories for PDBx/mmCIF and PDBML
> data files on the ftp archive.
>
> To help you prepare for these large structure entries with the new format
> extensions, we have created a set of PDBx/mmCIF and PDBML example files using
> data from existing large entries
> (http://mmcif.pdb.org/large-pdbx-examples/index.html). All these example
> files use 4-character chain identifiers to illustrate the upper limit of this
> extension. In the coming months, we plan to consolidate all divided/split
> entries in the archive into single PDBx/mmCIF and PDBML data files, which can
> be used for testing. Eventually, all “split” entries will be merged -and
> subsequently removed from the archive- and only the intact structures will be
> distributed by ftp. We will send another announcement describing the
> availability of these files. In the meantime we will be happy to answer any
> questions regarding the current examples at pdbx-annou...@mail.wwpdb.org.
>
> Best Regards,
>
> John Westbrook
>
>
> --
> John Westbrook
> RCSB, Protein Data Bank
> Rutgers, The State University of New Jersey
> Department of Chemistry and Chemical Biology
> 174 Frelinghuysen Rd Piscataway, NJ 08854-8087
> e-mail: jw...@rcsb.rutgers.edu
> Ph: (848) 445-4290 Fax: (732) 445-4320
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