[phenixbb] Question about writing cif files at the last round of refinement
pafonine at lbl.gov
Tue Nov 7 12:39:20 PST 2017
> 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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