[phenixbb] Question about writing cif files at the last round of refinement

Pavel Afonine pafonine at lbl.gov
Tue Nov 7 12:39:20 PST 2017

Hi Boaz,

> Perhaps I'm doing something wrong but  it seems as if I follow the 
> instructions correctly. To write cif files (data and  model) in the 
> final refinement run I tick the correct boxes in the output box of the 
> gui. I can see in the final.eff that this was accepted. However the 
> data cif file contains only the model derived quantities and not the 
> original Fobs, sigFobs etc. as they are on incoming mtz file. In the 
> next stage, as you propose, mmtbx.prepare_pdb_deposition routine 
> expects those quantities (i.e. Fobs etc.). I'm running the nightly 
> build 2919. Am I doing something wrong? I'd appreciate your advice.

first, you should tick two boxes: "Write final refined model into mmCIF 
file" and "Write Fobs, Fmodel and R-free-flags into mmCIF file". Then 
after refinement you should get two CIF files *_refine_*.cif (refined 
model) and *_refine_*.reflections.cif (reflections).

CIF with reflections contains these fields:


where F_meas_au is a name for Fobs (clearly, a weird way to name Fobs, 
not sure who invented it!).

This is what I get myself using the latest code. Is it different for you?

mmtbx.prepare_pdb_deposition seems to broken: I just ran a sample 
example where I asked to output model and reflection CIFs, and then 
supplied them to mmtbx.prepare_pdb_deposition and it crashed. Also, it 
crashes if I give it PDB and MTZ from refinement.


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