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

Paul Adams pdadams at lbl.gov
Tue Nov 7 14:24:53 PST 2017

mmtbx.prepare_pdb_deposition works for me in dev-2940 for files written from phenix.refine. You need to supply the sequence of the sample in a fasta file for it to write output. However, it shouldn’t crash. It won’t work with a PDB file, and an MTZ file is just used to pull symmetry and other info - the reflections aren’t combined with the model information in the output cif. 

> On Nov 7, 2017, at 12:39 PM, Pavel Afonine <PAfonine at lbl.gov> wrote:
> 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:
> loop_
>   _refln.index_h
>   _refln.index_k
>   _refln.index_l
>   _refln.F_meas_au
>   _refln.F_meas_sigma_au
>   _refln.pdbx_FWT
>   _refln.pdbx_PHWT
>   _refln.pdbx_DELFWT
>   _refln.pdbx_DELPHWT
>   _refln.pdbx_r_free_flag
>   _refln.status
>   _refln.pdbx_F_calc_with_solvent
>   _refln.pdbx_phase_calc_with_solvent
> 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.
> Pavel
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Paul Adams
Division Director, Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley Lab
Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab
Adjunct Professor, Department of Bioengineering, U.C. Berkeley
Vice President for Technology, the Joint BioEnergy Institute
Laboratory Research Manager, ENIGMA Science Focus Area

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