Hi,<br><br>We found this bug too, and fixed it over the weekend, so the very latest phenix nightly build should be OK. The indexing results themselves are not affected by the bug.<br><br>Nick Sauter<br><br><div class="gmail_quote">
On Tue, Jan 31, 2012 at 7:15 AM, Christian Roth <span dir="ltr"><<a href="mailto:christian.roth@bbz.uni-leipzig.de">christian.roth@bbz.uni-leipzig.de</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi,<br>
<br>
I had a few images, some of them are very bad. So itried to index 1 of the<br>
pictures, and indexing went very well, but then a strange error appeared which<br>
I cannot relate to anything.<br>
What might be the problem here?<br>
<br>
Best Regards<br>
<br>
Christian<br>
<br>
labelit.index_dev-968<br>
/hosts/vulcan1/mar345/moschuetz/064c2_4/064c2_4_001.mar2300<br>
<br>
<br>
Beam center is not immediately clear; rigorously retesting 2 solutions<br>
Beam x 172.5 y 172.9, initial score 405; refined rmsd: 0.1445 <Z>=20.4<br>
Beam x 171.8 y 175.6, initial score 335; refined rmsd: 0.2160 <Z>=14.9<br>
<br>
LABELIT Indexing results:<br>
Beam center x 172.58mm, y 172.91mm, distance 209.93mm ; 80% mosaicity=0.25<br>
deg.<br>
<br>
Solution Metric fit rmsd #spots crystal_system unit_cell<br>
volume<br>
:) 2 0.2528 dg 0.105 190 monoclinic mC 248.48 71.93 154.76<br>
90.00 112.70 90.00 2551913<br>
:) 1 0.0000 dg 0.076 203 triclinic aP 71.93 129.30 154.76<br>
111.69 90.25 106.07 1275944<br>
<br>
MOSFLM Integration results:<br>
Solution SpaceGroup Beam x y distance Resolution Mosaicity RMS<br>
:) 2 C2 172.89 172.41 209.92 2.54 0.250000 0.109<br>
1 P1 172.88 172.36 209.85 2.37 0.250000 0.094<br>
show_stack(1): /userdata-2/christian/phenix-<br>
dev-968/labelit/command_line/screen.py(84) top_level_indexing<br>
show_stack(2): /userdata-2/christian/phenix-dev-968/build/intel-<br>
linux-2.6/../../labelit/command_line/index.py(5) <module><br>
libc backtrace (28 frames, most recent call last):<br>
/userdata-2/christian/phenix-dev-968/build/intel-linux-2.6/base/bin/python<br>
[0x8058241]<br>
/lib/tls/i686/cmov/libc.so.6(__libc_start_main+0xe6) [0x4009fb56]<br>
/userdata-2/christian/phenix-dev-968/build/intel-<br>
linux-2.6/base/bin/python(main+0x17) [0x80582df]<br>
/userdata-2/christian/phenix-dev-968/build/intel-<br>
linux-2.6/base/bin/python(Py_Main+0xaba) [0x8058f2a]<br>
/userdata-2/christian/phenix-dev-968/build/intel-<br>
linux-2.6/base/bin/python(PyRun_SimpleFileExFlags+0xb5) [0x80f61fd]<br>
/userdata-2/christian/phenix-dev-968/build/intel-<br>
linux-2.6/base/bin/python(PyRun_FileExFlags+0xdc) [0x80f52cc]<br>
/userdata-2/christian/phenix-dev-968/build/intel-<br>
linux-2.6/base/bin/python(PyEval_EvalCode+0x22) [0x80d659e]<br>
/userdata-2/christian/phenix-dev-968/build/intel-<br>
linux-2.6/base/bin/python(PyEval_EvalCodeEx+0x603) [0x80d63f3]<br>
/userdata-2/christian/phenix-dev-968/build/intel-<br>
linux-2.6/base/bin/python(PyEval_EvalFrameEx+0x622e) [0x80d5ad6]<br>
/userdata-2/christian/phenix-dev-968/build/intel-<br>
linux-2.6/base/bin/python(PyEval_EvalFrameEx+0x3dc7) [0x80d366f]<br>
/userdata-2/christian/phenix-dev-968/build/intel-<br>
linux-2.6/base/bin/python(PyObject_Call+0x46) [0x806162a]<br>
/userdata-2/christian/phenix-dev-968/build/intel-linux-2.6/base/bin/python<br>
[0x8147760]<br>
/userdata-2/christian/phenix-dev-968/build/intel-<br>
linux-2.6/base/bin/python(PyEval_EvalCodeEx+0x4ba) [0x80d62aa]<br>
/userdata-2/christian/phenix-dev-968/build/intel-linux-2.6/base/bin/python<br>
[0x8145ea2]<br>
/userdata-2/christian/phenix-dev-968/build/intel-linux-2.6/base/bin/python<br>
[0x8064f09]<br>
/userdata-2/christian/phenix-dev-968/build/intel-linux-2.6/base/bin/python<br>
[0x8089ab0]<br>
/userdata-2/christian/phenix-dev-968/build/intel-linux-2.6/base/bin/python<br>
[0x8064f09]<br>
/userdata-2/christian/phenix-dev-968/build/intel-linux-2.6/base/bin/python<br>
[0x8089ab0]<br>
/userdata-2/christian/phenix-dev-968/build/intel-linux-2.6/base/bin/python<br>
[0x807b94a]<br>
/userdata-2/christian/phenix-dev-968/build/intel-linux-2.6/base/bin/python<br>
[0x80a3710]<br>
/userdata-2/christian/phenix-dev-968/build/intel-linux-2.6/base/bin/python<br>
[0x8089ab0]<br>
/userdata-2/christian/phenix-dev-968/build/intel-linux-2.6/base/bin/python<br>
[0x80a3677]<br>
/userdata-2/christian/phenix-dev-968/build/intel-<br>
linux-2.6/lib/libboost_python.so [0x4036b67b]<br>
/userdata-2/christian/phenix-dev-968/build/intel-<br>
linux-2.6/lib/cbflib_ext.so(boost::python::objects::value_holder<iotbx::detectors::Mar345Adaptor>::~value_holder()+0x4a)<br>
[0x42a13f22]<br>
/lib/tls/i686/cmov/libc.so.6(fclose+0x1a0) [0x400e4640]<br>
/lib/tls/i686/cmov/libc.so.6(fclose+0x41) [0x4018f241]<br>
[0x4001d400]<br>
/userdata-2/christian/phenix-dev-968/build/intel-<br>
linux-2.6/lib/boost_python_meta_ext.so(boost_adaptbx_segmentation_fault_backtrace+0x1f)<br>
[0x4032231f]<br>
Segmentation fault (Python and libc call stacks above)<br>
This crash may be due to a problem in any imported<br>
Python module, including modules which are not part<br>
of the cctbx project. To disable the traps leading<br>
to this message, define these environment variables<br>
(e.g. assign the value 1):<br>
BOOST_ADAPTBX_FPE_DEFAULT<br>
BOOST_ADAPTBX_SIGNALS_DEFAULT<br>
This will NOT solve the problem, just mask it, but<br>
may allow you to proceed in case it is not critical.<br>
<br>
--<br>
Christian Roth<br>
Institut für Bioanalytische Chemie<br>
Biotechnologisch-Biomedizinisches Zentrum<br>
Fakultät für Chemie und Mineralogie<br>
Universität Leipzig<br>
Deutscher Platz 5<br>
04103 Leipzig<br>
Telefon: +49 (0)341 97 31316<br>
Fax: +49 (0)341 97 31319<br>
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</blockquote></div><br><br clear="all"><br>-- <br>Nicholas K. Sauter, Ph. D.<br>Computer Staff Scientist, Physical Biosciences Division<div>Acting Head, Berkeley Center for Structural Biology<br>Lawrence Berkeley National Laboratory<br>
1 Cyclotron Rd., Bldg. 64R0121<br>Berkeley, CA 94720-8118<br>(510) 486-5713<br></div><br>