[phenixbb] phenix.refine crash due to MTZ input
Nathaniel Echols
nechols at lbl.gov
Wed Jan 23 16:30:44 PST 2013
On Wed, Jan 23, 2013 at 4:24 PM, wtempel <wtempel at gmail.com> wrote:
> this may perhaps fall under "garbage in, garbage out".
> The following reflection results in the appended stack trace.
> Would it be reasonable to instead just treat such reflection as missing?
If I'm reading the columns correctly, you should be able to refine
against F_r1lo1(+),SIGF_r1lo1(+),F_r1lo1(-),SIGF_r1lo1(-), which
probably won't have this problem. For a variety of reasons this is
often preferable to F,SIGF,DANO,SIGDANO anyway.
PS. you should update to 1.8.1 or the current nightly build.
-Nat
> Best regards,
> Wolfram Tempel
>
> <mtz.dmp>
> RFREE F_r1lo1 SIGF_r1lo1 DANO_r1lo1
> SIGDANO_r1lo1 F_r1lo1(+) SIGF_r1lo1(+) F_r1lo1(-)
> SIGF_r1lo1(-) ISYM_r1lo1 IMEAN_r1lo1 SIGIMEAN_r1lo1
> I_r1lo1(+) SIGI_r1lo1(+) I_r1lo1(-) SIGI_r1lo1(-)
> 20 4 54 11 None None -3.61389
> 15.223 19.349 9.78972 22.9629
> 11.6577 0 -227.641 69.6184
> -205.607 83.633 -277.365 125.635
>
> </mtz.dmp>
>
> <trace>
> Traceback (most recent call last):
> File
> "Blah/phenix-1.8-1069/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/refine.py",
> line 11, in <module>
> command_line.run(command_name="phenix.refine", args=sys.argv[1:])
> File "Blah/phenix-1.8-1069/phenix/phenix/refinement/command_line.py", line
> 74, in run
> master_params=customized_master_params)
> File "Blah/phenix-1.8-1069/phenix/phenix/refinement/command_line.py", line
> 274, in __init__
> reflection_file_server = self.reflection_file_server()
> File "Blah/phenix-1.8-1069/phenix/phenix/refinement/command_line.py", line
> 793, in reflection_file_server
> err=self.log)
> File "Blah/phenix-1.8-1069/cctbx_project/iotbx/reflection_file_utils.py",
> line 448, in __init__
> force_symmetry=self.force_symmetry))
> File "Blah/phenix-1.8-1069/cctbx_project/iotbx/reflection_file_reader.py",
> line 209, in as_miller_arrays
> base_array_info=base_array_info)
> File "Blah/phenix-1.8-1069/cctbx_project/iotbx/mtz/__init__.py", line 502,
> in as_miller_arrays
> dataset=dataset)
> File "Blah/phenix-1.8-1069/cctbx_project/iotbx/mtz/__init__.py", line 610,
> in group_columns
> group = self.extract_delta_anomalous(*labels)
> RuntimeError: cctbx Error: Invalid combination of values while extracting
> anomalous array from columns: F_r1lo1, SIGF_r1lo1, DANO_r1lo1,
> SIGDANO_r1lo1, hkl=(20,4,54) [tip: "phenix.mtz.dump --show_column_data
> file_name" is available for inspecting the MTZ file]
> </trace>
>
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