[phenixbb] mmCIF output _atom_site.B_iso_or_equiv

Dan McNamara dem at ucla.edu
Tue Feb 11 17:49:54 PST 2014

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.

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