[phenixbb] MemoryError in phenix.refine

[Pavel Afonine]

Hi,

calculation of "missing-Fobs-filled"  2mFo-DFc map is where it is most 
likely runs out of memory, since I compute per-residue map CC at this step.

Disabling output of "missing-Fobs-filled"  2mFo-DFc should help.

You can ask phenix.refine to output only two maps: 2mFo-DFc and mFo-DFc.

Pavel

On 9/5/11 9:13 AM, Tanner, John J. wrote:
> I get the following error at the end of a phenix.refine run.  The pdb file
> is produced, but the mtz file is empty.  The resolution is 1.15 A and the
> cell is
>
> CRYST1   84.808   93.803  132.080  90.00  90.00  90.00 P 21 21 21
>
> The version is
>
>    PHENIX: Python-based Hierarchical ENvironment for Integrated Xtallography
>    Version: 1.7.1
>    Release tag: 743
>    Platform: intel-linux-2.6 redhat-e5.6
>
> I've seen this sort of thread on the bb previously.  Is there a fix for
> this, other than using refmac?
>
> Thanks.
>
>
> Traceback (most recent call last):
>    File "/linux/src/phenix-1.7.1-743/phenix/phenix/command_line/refine.py",
> line 11, in<module>
>      command_line.run(command_name="phenix.refine", args=sys.argv[1:])
>    File
> "/linux/src/phenix-1.7.1-743/phenix/phenix/refinement/command_line.py", line
> 107, in run
>      map_manger.write_files()
>    File "/linux/src/phenix-1.7.1-743/phenix/phenix/refinement/driver.py",
> line 1430, in write_files
>      map_coeff_dataset=self.write_mtz_file(),
>    File "/linux/src/phenix-1.7.1-743/phenix/phenix/refinement/driver.py",
> line 1419, in write_mtz_file
>      params = self.map_params.map_coefficients)
>    File "/linux/src/phenix-1.7.1-743/cctbx_project/mmtbx/maps/__init__.py",
> line 512, in __init__
>      coeffs = map_coefficients_from_fmodel(fmodel = fmodel, params = mcp)
>    File "/linux/src/phenix-1.7.1-743/cctbx_project/mmtbx/maps/__init__.py",
> line 359, in map_coefficients_from_fmodel
>      fill_mode          = "dfmodel")
>    File "/linux/src/phenix-1.7.1-743/cctbx_project/mmtbx/f_model.py", line
> 1920, in electron_density_map
>      fill_mode              = fill_mode)
>    File "/linux/src/phenix-1.7.1-743/cctbx_project/mmtbx/map_tools.py", line
> 137, in __init__
>      self.fmodel = self.fmodel.fill_missing_f_obs(fill_mode = fill_mode)
>    File "/linux/src/phenix-1.7.1-743/cctbx_project/mmtbx/f_model.py", line
> 1681, in fill_missing_f_obs
>      fmodel=self, fill_mode=fill_mode)
>    File
> "/linux/src/phenix-1.7.1-743/cctbx_project/mmtbx/missing_reflections_handler
> .py", line 129, in fill_missing_f_obs
>      fmodel = select_by_map_cc(fmodel = fmodel.deep_copy()))
>    File
> "/linux/src/phenix-1.7.1-743/cctbx_project/mmtbx/missing_reflections_handler
> .py", line 113, in select_by_map_cc
>      update_f_mask = True)
>    File "/linux/src/phenix-1.7.1-743/cctbx_project/mmtbx/f_model.py", line
> 723, in update_xray_structure
>      force_update   = force_update_f_mask)
>    File "/linux/src/phenix-1.7.1-743/cctbx_project/mmtbx/masks.py", line 268,
> in shell_f_masks
>      self.compute_f_mask()
>    File "/linux/src/phenix-1.7.1-743/cctbx_project/mmtbx/masks.py", line 321,
> in compute_f_mask
>      fm_asu = asu_mask_obj.structure_factors(self.miller_array.indices(),i+1)
> MemoryError
>
>
>