Thanks Pavel.
I set fill_missing_f_obs = False in the block below, and that seems to work. Is that what you meant by "Disabling output of "missing-Fobs-filled" 2mFo-DFc"?
map_coefficients {
map_type = "2mFo-DFc"
format = *mtz phs
mtz_label_amplitudes = "2FOFCWT"
mtz_label_phases = "PH2FOFCWT"
kicked = False
fill_missing_f_obs = False
acentrics_scale = 2
centrics_pre_scale = 1
sharpening = False
sharpening_b_factor = None
exclude_free_r_reflections = False
isotropize = True
resharp_after_isotropize = False
dev {
complete_set_up_to_d_min = False
aply_same_incompleteness_to_complete_set_at = randomly low high
}
}
On 9/5/11 12:01 PM, "Pavel Afonine"
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
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