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Tim, PDB file format is good because of its simplicity and that's perhaps it. However, it cannot accommodate wealth of information that is available at the end of refinement. Of course one can keep creating remarks for PDB file etc but I guess mmCIF is just a better way of doing it rather than uglify existing PDB format by countless decorators. Editing (for example, PDB files) by hand is a questionable practice. If you know programming use either existing reliable parsers (available for both, PDB and CIF) or write your own jiffy. phenix.refine and surrounding tools can input and output both, PDB and mmCIF (both, model and reflections). Pavel On Mon, Aug 5, 2013 at 1:03 AM, Tim Gruene <[log in to unmask]> wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > Dear all, > > having read Gerard Kleywegt's latest announcement on the wwPDB Workshop > (1st August) made me wonder whether it is planned to introduce mmCIF as > working format to users in addition to using it at e.g. the PDB, because > I think that would make life unnecessarily complicated. > > The example mmCIF file for GroEL is about 7.5 times bigger than its PDB > file. > I know that disk space is 'cheap' nowadays, but that does not make it fast. > > And personally I find mmCIF very awkward to work with, since it is not > line-oriented. 'grep', 'awk', 'perl' etc. do not work well on XML-like > files. > Instead of using mmCIF, one could, e.g. introduce a free format PDB > format, with space holders for non-assigned entities, and maybe a line > continuation character. > > If mmCIF is not going to be the working format for MX (refinement) > programs I would be happy for a reassurance, and otherwise I would > appreciate some comments about the benefits of an XML file format over a > line-oriented free format for the scientists that work with structural > data. > I my opinion, using XML (or mmCIF) for structural information is an > attempt of programmers to make themselves more indespensable to > scientists, rather than scientifically needed. > > Best, > Tim > > - -- > - -- > Dr Tim Gruene > Institut fuer anorganische Chemie > Tammannstr. 4 > D-37077 Goettingen > > GPG Key ID = A46BEE1A > > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.14 (GNU/Linux) > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ > > iD8DBQFR/1xbUxlJ7aRr7hoRAkLNAKClH9RpAA7NJsH3YFOTguOo9kjwoQCZAf/m > JF1oyJNuq+8b+VsywDupElo= > =bvb3 > -----END PGP SIGNATURE----- >