Hi Oliver, yes, model files in mmCIF are supported. I just verified it myself by running a dummy phenix.real_space_refine run using a map and mmCIF file and it runs fine. I can have a look at your mmCIF file.. Pavel On 2/11/16 16:07, Oliver Clarke wrote:

Hello, Is it possible to use phenix.real_space_refine with mmcif input?

When I attempt to run as "phenix.real_space_refine model.mmcif map.mrc" or "phenix.real_space_refine model.cif map.mrc" I get the error "Sorry: PDB file is needed", and looking at the documentation I cannot see how to explicitly specify the model (there is not "model" keyword or similar).

Anybody have a way around this? Or is there a keyword I am missing? phenix.refine generally works fine with mmcif, but maybe real_space_refine has not been configured to do so yet? Would be helpful for large structures which break the regular pdb format if so.

Cheers, Oli

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