[phenixbb] MemoryError in phenix.refine

[Tanner, John J.]

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



-- 
John J. Tanner
Professor of Chemistry and Biochemistry
University of Missouri-Columbia
125 Chemistry Building
Columbia, MO 65211
Phone: 573-884-1280
Fax: 573-882-2754
Email: tannerjj at missouri.edu
http://www.chem.missouri.edu/TannerGroup/tanner.html