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