[phenixbb] map error?

Christian Roth christian.roth at bbz.uni-leipzig.de
Thu May 19 01:15:29 PDT 2011


Dear all,

I got a error message in the last round of phenix.refine which seesm to be 
related to map or mtz file creation (error.txt attached). I used the GUI and I 
unchecked the map creation option in ccp4 or Xplor before I started the run.  
I am not sure whats going wrong here. 
Please could you point me to the problem.

Best regards

Christian
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RuntimeError : scitbx array_family range error
Traceback:
  File "/userdata-2/christian/phenix-1.7.1-743/cctbx_project/libtbx/thread_utils.py", line 223, in run
    return_value = self._target(self._args, self._kwargs, self._c)

  File "/userdata-2/christian/phenix-1.7.1-743/cctbx_project/libtbx/runtime_utils.py", line 58, in __call__
    result = self.target()

  File "/userdata-2/christian/phenix-1.7.1-743/phenix/phenix/refinement/runtime.py", line 68, in __call__
    call_back_handler=callback)

  File "/userdata-2/christian/phenix-1.7.1-743/phenix/phenix/refinement/command_line.py", line 107, in run
    map_manger.write_files()

  File "/userdata-2/christian/phenix-1.7.1-743/phenix/phenix/refinement/driver.py", line 1430, in write_files
    map_coeff_dataset=self.write_mtz_file(),

  File "/userdata-2/christian/phenix-1.7.1-743/phenix/phenix/refinement/driver.py", line 1419, in write_mtz_file
    params = self.map_params.map_coefficients)

  File "/userdata-2/christian/phenix-1.7.1-743/cctbx_project/mmtbx/maps/__init__.py", line 512, in __init__
    coeffs = map_coefficients_from_fmodel(fmodel = fmodel, params = mcp)

  File "/userdata-2/christian/phenix-1.7.1-743/cctbx_project/mmtbx/maps/__init__.py", line 394, in map_coefficients_from_fmodel
    resharp    = params.resharp_after_isotropize).map_coeffs

  File "/userdata-2/christian/phenix-1.7.1-743/cctbx_project/mmtbx/map_tools.py", line 50, in __init__
    data = self.map_coeffs.data()*isotropize_helper.iso_scale.data())



Platform info:
__FILE__ = /net/longnose/scratch2/phenix/phenix-1.7.1-743/cctbx_project/boost_adaptbx/meta_ext.cpp
__DATE__ = Apr 28 2011
__TIME__ = 01:20:17
__i386__
__linux
__GNUC__ = 3
__GNUC_MINOR__ = 4
__GNUC_PATCHLEVEL__ = 2
boost::python::cxxabi_cxa_demangle_is_broken(): false
__GXX_WEAK__ = 1
__VERSION__ = 3.4.2 20041017 (Red Hat 3.4.2-6.fc3)
FE_INEXACT = 32
FE_DIVBYZERO = 4
FE_UNDERFLOW = 16
FE_OVERFLOW = 8
FE_INVALID = 1
FE_ALL_EXCEPT = 61
BOOST_LIB_VERSION = 1_47
PY_VERSION = 2.7.1
PYTHON_API_VERSION = 1013
sizeof(bool) = 1
sizeof(short) = 2
sizeof(int) = 4
sizeof(long) = 4
sizeof(std::size_t) = 4
sizeof(void*) = 4
sizeof(long long) = 8
sizeof(float) = 4
sizeof(double) = 8
sizeof(long double) = 12
sizeof(boost::int32_t) = 4
sizeof(boost::uint32_t) = 4
sizeof(wchar_t) = 4
__PTRDIFF_TYPE__
Py_USING_UNICODE
sizeof(PY_UNICODE_TYPE) = 2
gnu libc version: 2.10.1
BOOST_ADAPTBX_TYPE_ID_SIZE_T_EQ_UNSIGNED
os.name: posix
sys.platform: linux2
sys.byteorder: little
platform.platform(): Linux-2.6.31-23-generic-pae-i686-with-debian-squeeze-sid
platform.architecture(): ('32bit', 'ELF')
floating_point_exceptions.division_by_zero_trapped: False
floating_point_exceptions.invalid_trapped: False
floating_point_exceptions.overflow_trapped: False
number of processors: 8
Memory total:  25,405,636,608
Memory free:   21,668,925,440
import thread: OK
"hello" = ['h', 'e', 'l', 'l', 'o']
u"hello" = ['h', '\x00', 'e', '\x00', 'l', '\x00', 'l', '\x00', 'o', '\x00']
u"\u00C5" = ['\xc5', '\x00'] as utf-8 = ['\xc3', '\x85']
LATIN CAPITAL LETTER A WITH RING ABOVE = ?


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