[phenixbb] Calculate average B-factor?

Nathaniel Echols nechols at lbl.gov
Sun Oct 5 10:34:06 PDT 2014

On Sun, Oct 5, 2014 at 2:18 AM, Tim Gruene <tg at 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

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.

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