[phenixbb] Using phenix.real_space_refine with mmcif model?

Pavel Afonine pafonine at lbl.gov
Mon Feb 15 23:12:22 PST 2016

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..


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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