[Pipet Devel] Loci markup language and infrastructure things

[Konrad Hinsen]

> Also, for structure, there don't appear to be any MLs even attempting to
> do this, with the exception of CML. So, my idea is to take the PDB file
> format and XMLize it. If any of you know any glaring holes in PDB let
> me know, and we can work around those.

During a visit at EMBL last week, I talked to some people who are
working on an mmCIF to XML converter, using an XML version of the
mmCIF dictionary (no DTD yet, but it is planned). The goal is to save
everybody else the work of writing a parser for the STAR format that
CIF and mmCIF are based on. XML parsers are much more widely
available.

I can't judge how eager the crystallography community is to move to
mmCIF, but from what I heard at EMBL, it seems that mmCIF is getting
more and more attention - the PDB will finally accept submitted mmCIF
files which contain information that cannot easily be converted to PDB
format. So I think it's worth waiting for the mmCIF/XML stuff (which
is supposed to be ready soon) instead of doing our own format based on
the less flexible PDB format.

As for glaring holes in PDB, I think there are many, although
mostly related to the rather loose interpretation of the format
description that most programs have applied.

Konrad.
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