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

[Felix Höfling]

Am 10.07.2014, 08:39 Uhr, schrieb Konrad Hinsen  
<address@hidden>:

> Felix Höfling writes:
>
>  > From Olaf (whom I consider an expert in PDB) I got the information
>  > that PDB only stores connections, no bond types.
>
> The PDB file format only stores connections. The PDB database also
> stores bond types, and makes them available in the mmCIF and PDBML
> files. The bond types are 'sing', 'doub', 'trip', 'quad', and 'arom',
> which all make sense only at the atomic scale.
>
> The PDB file format is not a good reference. It's completely outdated
> and insufficient. Even the PDB doesn't want it any more.
>
> Konrad.

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

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.

To be realistic, we need somebody from the protein community to get  
excited about H5MD and to join ...

Felix