[phenixbb] labelit.index python error

[Christian Roth]

Hi,

I had a few images, some of them are very bad. So itried to index 1 of the 
pictures, and indexing went very well, but then a strange error appeared which 
I cannot relate to anything. 
What might be the problem here?

Best Regards 

Christian

labelit.index_dev-968 
/hosts/vulcan1/mar345/moschuetz/064c2_4/064c2_4_001.mar2300


Beam center is not immediately clear; rigorously retesting 2 solutions
Beam x 172.5 y 172.9, initial score 405; refined rmsd: 0.1445 <Z>=20.4
Beam x 171.8 y 175.6, initial score 335; refined rmsd: 0.2160 <Z>=14.9

LABELIT Indexing results:
Beam center x  172.58mm, y  172.91mm, distance  209.93mm ; 80% mosaicity=0.25 
deg.

Solution  Metric fit  rmsd  #spots  crystal_system   unit_cell                                  
volume
:)   2     0.2528 dg 0.105    190    monoclinic mC  248.48  71.93 154.76  
90.00 112.70  90.00  2551913
:)   1     0.0000 dg 0.076    203     triclinic aP   71.93 129.30 154.76 
111.69  90.25 106.07  1275944

MOSFLM Integration results:
Solution  SpaceGroup Beam x   y  distance  Resolution Mosaicity RMS
:)   2           C2 172.89 172.41  209.92       2.54    0.250000    0.109
     1           P1 172.88 172.36  209.85       2.37    0.250000    0.094
show_stack(1): /userdata-2/christian/phenix-
dev-968/labelit/command_line/screen.py(84) top_level_indexing
show_stack(2): /userdata-2/christian/phenix-dev-968/build/intel-
linux-2.6/../../labelit/command_line/index.py(5) <module>
libc backtrace (28 frames, most recent call last):
  /userdata-2/christian/phenix-dev-968/build/intel-linux-2.6/base/bin/python 
[0x8058241]
  /lib/tls/i686/cmov/libc.so.6(__libc_start_main+0xe6) [0x4009fb56]
  /userdata-2/christian/phenix-dev-968/build/intel-
linux-2.6/base/bin/python(main+0x17) [0x80582df]
  /userdata-2/christian/phenix-dev-968/build/intel-
linux-2.6/base/bin/python(Py_Main+0xaba) [0x8058f2a]
  /userdata-2/christian/phenix-dev-968/build/intel-
linux-2.6/base/bin/python(PyRun_SimpleFileExFlags+0xb5) [0x80f61fd]
  /userdata-2/christian/phenix-dev-968/build/intel-
linux-2.6/base/bin/python(PyRun_FileExFlags+0xdc) [0x80f52cc]
  /userdata-2/christian/phenix-dev-968/build/intel-
linux-2.6/base/bin/python(PyEval_EvalCode+0x22) [0x80d659e]
  /userdata-2/christian/phenix-dev-968/build/intel-
linux-2.6/base/bin/python(PyEval_EvalCodeEx+0x603) [0x80d63f3]
  /userdata-2/christian/phenix-dev-968/build/intel-
linux-2.6/base/bin/python(PyEval_EvalFrameEx+0x622e) [0x80d5ad6]
  /userdata-2/christian/phenix-dev-968/build/intel-
linux-2.6/base/bin/python(PyEval_EvalFrameEx+0x3dc7) [0x80d366f]
  /userdata-2/christian/phenix-dev-968/build/intel-
linux-2.6/base/bin/python(PyObject_Call+0x46) [0x806162a]
  /userdata-2/christian/phenix-dev-968/build/intel-linux-2.6/base/bin/python 
[0x8147760]
  /userdata-2/christian/phenix-dev-968/build/intel-
linux-2.6/base/bin/python(PyEval_EvalCodeEx+0x4ba) [0x80d62aa]
  /userdata-2/christian/phenix-dev-968/build/intel-linux-2.6/base/bin/python 
[0x8145ea2]
  /userdata-2/christian/phenix-dev-968/build/intel-linux-2.6/base/bin/python 
[0x8064f09]
  /userdata-2/christian/phenix-dev-968/build/intel-linux-2.6/base/bin/python 
[0x8089ab0]
  /userdata-2/christian/phenix-dev-968/build/intel-linux-2.6/base/bin/python 
[0x8064f09]
  /userdata-2/christian/phenix-dev-968/build/intel-linux-2.6/base/bin/python 
[0x8089ab0]
  /userdata-2/christian/phenix-dev-968/build/intel-linux-2.6/base/bin/python 
[0x807b94a]
  /userdata-2/christian/phenix-dev-968/build/intel-linux-2.6/base/bin/python 
[0x80a3710]
  /userdata-2/christian/phenix-dev-968/build/intel-linux-2.6/base/bin/python 
[0x8089ab0]
  /userdata-2/christian/phenix-dev-968/build/intel-linux-2.6/base/bin/python 
[0x80a3677]
  /userdata-2/christian/phenix-dev-968/build/intel-
linux-2.6/lib/libboost_python.so [0x4036b67b]
  /userdata-2/christian/phenix-dev-968/build/intel-
linux-2.6/lib/cbflib_ext.so(boost::python::objects::value_holder<iotbx::detectors::Mar345Adaptor>::~value_holder()+0x4a) 
[0x42a13f22]
  /lib/tls/i686/cmov/libc.so.6(fclose+0x1a0) [0x400e4640]
  /lib/tls/i686/cmov/libc.so.6(fclose+0x41) [0x4018f241]
  [0x4001d400]
  /userdata-2/christian/phenix-dev-968/build/intel-
linux-2.6/lib/boost_python_meta_ext.so(boost_adaptbx_segmentation_fault_backtrace+0x1f) 
[0x4032231f]
Segmentation fault (Python and libc call stacks above)
                This crash may be due to a problem in any imported
                Python module, including modules which are not part
                of the cctbx project. To disable the traps leading
                to this message, define these environment variables
                (e.g. assign the value 1):
                    BOOST_ADAPTBX_FPE_DEFAULT
                    BOOST_ADAPTBX_SIGNALS_DEFAULT
                This will NOT solve the problem, just mask it, but
                may allow you to proceed in case it is not critical.

-- 
Christian Roth
Institut für Bioanalytische Chemie
Biotechnologisch-Biomedizinisches Zentrum
Fakultät für Chemie und Mineralogie
Universität Leipzig
Deutscher Platz 5
04103 Leipzig
Telefon: +49 (0)341 97 31316
Fax: +49 (0)341 97 31319