[phenixbb] MemoryError in phenix.refine

Pavel Afonine pafonine at lbl.gov
Mon Sep 5 12:36:40 PDT 2011


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"<pafonine at lbl.gov>  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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