Re: [phenixbb] error after adp refinement

Hi Nat, fixed in the latest build. Thanks a lot and best wishes Christian Am Donnerstag 08 März 2012 15:14:25 schrieb Nathaniel Echols:

Please update to the latest nightly build (1000!) - I think either Pavel or I fixed this a few weeks ago. (But if not, let us know ASAP.)

-Nat

On Thu, Mar 8, 2012 at 5:37 AM, Christian Roth

wrote:

...

Dear Phenix Team, I started a refinement with anisotropic adp and weight optimization and directly after the optimization step an error appeared which never appeared befor for me. The previous steps of mask optimization and xyz refinement worked well.

Best Regards

Christian

AssertionError : Traceback: File "/userdata-2/christian/phenix- dev-979/cctbx_project/libtbx/thread_utils.py", line 229, in run return_value = self._target(self._args, self._kwargs, self._c)

File "/userdata-2/christian/phenix- dev-979/cctbx_project/libtbx/runtime_utils.py", line 72, in __call__ result = self.target()

File "/userdata-2/christian/phenix- dev-979/phenix/phenix/refinement/runtime.py", line 68, in __call__ call_back_handler=callback)

File "/userdata-2/christian/phenix- dev-979/phenix/phenix/refinement/command_line.py", line 97, in run call_back_handler=call_back_handler)

File "/userdata-2/christian/phenix- dev-979/phenix/phenix/refinement/driver.py", line 1494, in run ncs_manager = self.ncs_manager)

File "/userdata-2/christian/phenix- dev-979/phenix/phenix/refinement/strategies.py", line 1046, in refinement_machine h_params = h_params)

File "/userdata-2/christian/phenix- dev-979/cctbx_project/mmtbx/refinement/adp_refinement.py", line 212, in __init__ nproc = nproc)

File "/userdata-2/christian/phenix- dev-979/cctbx_project/mmtbx/refinement/adp_refinement.py", line 389, in __init__ compute_gradients=False).target_work())

Platform info: __FILE__ = /net/longnose/scratch2/phenix/phenix- dev-979/cctbx_project/boost_adaptbx/meta_ext.cpp __DATE__ = Feb 7 2012 __TIME__ = 02:05:24 __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: 2.10.1 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: 20,305,633,280 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 = Å

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