On Sun, Oct 5, 2014 at 2:18 AM, Tim Gruene <tg@shelx.uni-ac.gwdg.de> wrote:

reading this beauty I would like to ask a question to the respective
developers:
Will the PDB format remain the working format for the users and only
upon deposition will it be converted to PDBml for archiving purposes, or
are the refinement programs (et al.) going to abandon PDB, too?

We certainly have no plans to abandon PDB format entirely. I think over the long term what will happen is that programs will start adding optional features that require the use of mmCIF, and eventually mmCIF will become the default working format. This requires that we first convert all of our code to parse and use the advanced features of mmCIF internally, which will take some time. Whether the programs will have an option to output PDB files or whether you'll just need to use phenix.cif_as_pdb first is undecided. But this is thinking years in the future. What we probably won't be doing is trying to cram more and more information into REMARK records.

My understanding was that the PDB was going to require that you deposit mmCIF files in the very near future - not converting them internally. Now that phenix.refine and Refmac can output mmCIF directly, there's really no reason to still deposit PDB and MTZ format.

-Nat