[phenixbb] MemoryError in phenix.refine
Tanner, John J.
TannerJJ at missouri.edu
Mon Sep 5 09:13:40 PDT 2011
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
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