[phenixbb] mmCIF output _atom_site.B_iso_or_equiv

[Pavel Afonine]

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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