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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:
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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

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