[phenixbb] phenix-1.7.2-x refine error

Christoph Parthier cparthier at googlemail.com
Thu Nov 24 09:46:52 PST 2011


Dear Phenix developers,

Using the current phenix version, refinements of a 'certain structure' 
always stop with the error message quoted below, while the refinement of 
other 'similar structures' work flawlessly.

In the error case the three scheduled macrocycles of refinement seem to 
finish (the refined PDB is there) but at there seems to be problem in 
finishing the job - the output MTZ file has zero byte length and the 
last line in refine.log is:

============================== Exporting results 
==============================



This occurs with several 1.7.2-x versions of phenix, I'm not sure about 
1.7.1-x. Interestingly, the 'problem structure' can be refined without 
problems using the same input files in phenix-1.7-650.

Any idea whether this is due to an installation problem or a bug?

Thanks,
Christoph

Here's the error message:


MemoryError :
Traceback:
   File "/cryst/phenix-1.7.2-869/cctbx_project/libtbx/thread_utils.py", 
line 229, in run
     return_value = self._target(self._args, self._kwargs, self._c)

   File "/cryst/phenix-1.7.2-869/cctbx_project/libtbx/runtime_utils.py", 
line 72, in __call__
     result = self.target()

   File "/cryst/phenix-1.7.2-869/phenix/phenix/refinement/runtime.py", 
line 67, in __call__
     call_back_handler=callback)

   File 
"/cryst/phenix-1.7.2-869/phenix/phenix/refinement/command_line.py", line 
115, in run
     map_manger.write_files()

   File "/cryst/phenix-1.7.2-869/phenix/phenix/refinement/driver.py", 
line 1535, in write_files
     map_coeff_dataset=self.write_mtz_file(),

   File "/cryst/phenix-1.7.2-869/phenix/phenix/refinement/driver.py", 
line 1524, in write_mtz_file
     params = self.map_params.map_coefficients)

   File "/cryst/phenix-1.7.2-869/cctbx_project/mmtbx/maps/__init__.py", 
line 502, in __init__
     coeffs = map_coefficients_from_fmodel(fmodel = fmodel, params = mcp)

   File "/cryst/phenix-1.7.2-869/cctbx_project/mmtbx/maps/__init__.py", 
line 353, in map_coefficients_from_fmodel
     fill_mode          = "dfmodel")

   File "/cryst/phenix-1.7.2-869/cctbx_project/mmtbx/f_model.py", line 
1887, in electron_density_map
     fill_mode              = fill_mode)

   File "/cryst/phenix-1.7.2-869/cctbx_project/mmtbx/map_tools.py", line 
114, in __init__
     update_scaling = update_scaling)

   File "/cryst/phenix-1.7.2-869/cctbx_project/mmtbx/f_model.py", line 
1663, in fill_missing_f_obs
     fmodel=self, fill_mode=fill_mode, update_scaling=update_scaling)

   File 
"/cryst/phenix-1.7.2-869/cctbx_project/mmtbx/missing_reflections_handler.py", 
line 131, in fill_missing_f_obs
     fmodel = select_by_map_cc(fmodel = fmodel.deep_copy()))

   File 
"/cryst/phenix-1.7.2-869/cctbx_project/mmtbx/missing_reflections_handler.py", 
line 85, in select_by_map_cc
     fourier_coefficients = coeffs)

   File 
"/cryst/phenix-1.7.2-869/cctbx_project/cctbx/miller/__init__.py", line 
3688, in __init__
     conjugate_flag=True)



Platform info:
__FILE__ = 
/net/longnose/scratch2/phenix/phenix-1.7.2-869/cctbx_project/boost_adaptbx/meta_ext.cpp
__DATE__ = Sep 23 2011
__TIME__ = 00:13:14
__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_48
PY_VERSION = 2.7.2
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: 2.6.1
BOOST_ADAPTBX_TYPE_ID_SIZE_T_EQ_UNSIGNED
os.name: posix
sys.platform: linux2
sys.byteorder: little
platform.platform(): 
Linux-2.6.22.13-GOLIAT-0.3-bigsmp-i686-with-SuSE-10.3-i586
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:  4,238,028,800
Memory free:   3,715,174,400
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 = Ã



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