Re: [h5md-user] Tuples and topology, the return

[Konrad Hinsen]

Felix Höfling writes:

 > What I understand is that PDB is still the prevailing format for protein  
 > data, but nobody likes it. Does the PDB offer alternatives yet?

The PDB has been promoting mmCIF as a replacement for the PDB format
for about 15 years. They also jumped on the XML bandwagon and
introduced PDBML as an alternative. Both mmCIF and PDBML files contain
the full information stored in the database, much more than the
PDB files can handle. And both are very well documented.

mmCIF has had a big acceptance problem, because nobody wanted to
change their software. But the problems with the PDB format are very
real as well. The PDB has finally decided to drop support for PDB
files in 2016.

 > I wasn't aware that the PDB files come with a bundle of
 > complementary file formats. This information, of course, should be
 > combined in a single H5MD file. If other short-comings of PDB
 > could be fixed on the way this would be great. I think it is a
 > worthwile goal for H5MD to potentially become a standard container
 > for protein data.

An mmCIF file contains everything. And H5MD cannot handle any of the
information in a PDB entry. There is no overlap at the current stage
of H5MD.

Konrad
-- 
---------------------------------------------------------------------
Konrad Hinsen
Centre de Biophysique Moléculaire, CNRS Orléans
Synchrotron Soleil - Division Expériences
Saint Aubin - BP 48
91192 Gif sur Yvette Cedex, France
Tel. +33-1 69 35 97 15
E-Mail: research AT khinsen DOT fastmail DOT net
http://dirac.cnrs-orleans.fr/~hinsen/
ORCID: http://orcid.org/0000-0003-0330-9428
Twitter: @khinsen
---------------------------------------------------------------------