Hi Oliver,

Thank you for pointing this out. We will work on this and this feature should become available shortly.

Meanwhile, I would recommend to use phenix.pdb_as_cif command-line tool to convert pdb files to mmcif as it would preserve more information (for example, secondary structure annotations).

Best regards,

Oleg Sobolev.

On Sat, Sep 24, 2016 at 2:22 AM, Oliver Clarke <olibclarke@gmail.com> wrote:

Any chance of getting mmcif output in phenix.real_space_refine? Or does it exist and I have just overlooked the option? Right now I can use mmcif as input, but the refined coordinates are still written as pdb (hybrid32). The PDB unfortunately doesn’t accept hybrid32, so I always need to convert to mmcif with phenix.pdbtools prior to deposition - no big deal but would make life easier for large-ish structures.

Cheers
Oli.
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