Hi John, yes. Pavel On 9/5/11 10:53 AM, Tanner, John J. wrote:

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" wrote:

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

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