On Tue, Jan 31, 2012 at 7:15 AM, Christian Roth <christian.roth@bbz.uni-leipzig.de> wrote:

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
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