File formats

Many of our facilities have their own file format. Sorry for that, but in all those cases where there existed no standard, we had to do something...

The formats for each facility are described at the page related to that facility. That leaves the PDB format undescribed, so we explain here our views on that topic.

PDB files come in two flavours, the punched card format from the 70's, and the mmCIF format that now is also already more than a decade old. The PDB has in 2014 officially converted from the punched card format to the mmCIF format. Given that we do not yet know software from outside our own group that actually uses the mmCIF format, it seems unlikely that anybody will need protein structure coordinate files in the mmCIF format any time soon.

The CMBI is ready to make the conversion. If, one day, PDB files will stop being provided by the wwPDB in the old punched card format then we can produce all entries of all facilities using mmCIF files as input. Over the next three years we will double all facilities that provide protein structure coordinates as output; these will in due time all be delivered in the old punched card format and in the new mmCIF format.

If anybody really needs mmCIF formatted files, then we will put the production of those files high on the priority list. For now, we suggest that people use any of the mmCIF-PDB converters, like the one made freely available by the CCP4.