[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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