Hi Dan, I'm not sure I understand what you mean by "B-factors reported in the .cif output are not consistent with those in the .pdb output from phenix.refine"... Could you please send me CIF and PDB files off list? Pavel On 2/11/14, 5:49 PM, Dan McNamara wrote:
Hi all,
I have a structure with 96 chains in the ASU and mmCIF format is required for using the RCSB PDB software tools with two-letter chain IDs. That's all fine, but when I use the argument "output.write_model_cif_file=True" with my refinement run, the B-factors reported in the .cif output are not consistent with those in the .pdb output from phenix.refine. Trying to deposit the mmCIF output with U=0.00008 flags their returned final .PDB copy as 0.00.
Is there functionality for having the isotropic B-factor equivalent recorded for mmCIF format output?
I have not found a way to parameterize phenix.pdbtools so that the mmCIF output has the B-factor the PDB is looking for, and all the information desired from the phenix.refine mmCIF output. I can use "convert to isotropic" and output as mmCIF, but then the ANISOU information from TLS refinement is not retained.
Best, Dan
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