[phenixbb] NCS error in Phenix 1.7.1-743

Ngan Nguyen Bich ngan.nguyenbich at student.kuleuven.be
Fri Jun 24 01:07:12 PDT 2011


Dear all,

I've got a problem when rerunning the same job of my project in the new laptop. I've found that it's because of the NCS restraint groups set-up

In the old computer I set two NCS restraints groups as:
First group:
Reference group: chain A and sidechain and resid 3:216 and not (resid 63 or resid 66 or resid 81 or resid 93 or resid 133 or resid 135 or resid 181 or resid 184 or resid 193 or resid 194 or resid 212)
Second group:
Reference group: chain A and backbone and resid 3:217 and not (resid 63 or resid 133 or resid 135 or resid 184)
And the refine_phenix run well in the old computer, but the new laptop with the error in the end of this letter.
I've found that if I delete the backbone in the second group, it runs again. So I wonder that how I could refine NCS restraint of backbone now?

Thank you in advance.
Ngan

RuntimeError : mean() argument is an empty array
Traceback:
  File "/Applications/PHENIX-1.7.1-743/Contents/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 "/Applications/PHENIX-1.7.1-743/Contents/phenix-1.7.1-743/cctbx_project/libtbx/runtime_utils.py", line 58, in __call__
    result = self.target()

  File "/Applications/PHENIX-1.7.1-743/Contents/phenix-1.7.1-743/phenix/phenix/refinement/runtime.py", line 68, in __call__
    call_back_handler=callback)

  File "/Applications/PHENIX-1.7.1-743/Contents/phenix-1.7.1-743/phenix/phenix/refinement/command_line.py", line 89, in run
    call_back_handler=call_back_handler)

  File "/Applications/PHENIX-1.7.1-743/Contents/phenix-1.7.1-743/phenix/phenix/refinement/driver.py", line 1278, in run
    reference_model_manager = self.reference_model_manager)

  File "/Applications/PHENIX-1.7.1-743/Contents/phenix-1.7.1-743/phenix/phenix/refinement/strategies.py", line 322, in refinement_machine
    monitors.collect(step = "0    :", model = model, fmodels = fmodels)

  File "/Applications/PHENIX-1.7.1-743/Contents/phenix-1.7.1-743/cctbx_project/mmtbx/refinement/__init__.py", line 51, in collect
    rigid_body_shift_accumulator = rigid_body_shift_accumulator)

  File "/Applications/PHENIX-1.7.1-743/Contents/phenix-1.7.1-743/cctbx_project/mmtbx/refinement/print_statistics.py", line 263, in collect
    ignore_side_chain = True,

  File "/Applications/PHENIX-1.7.1-743/Contents/phenix-1.7.1-743/cctbx_project/mmtbx/model.py", line 971, in geometry_statistics
    restraints_manager = self.restraints_manager)

  File "/Applications/PHENIX-1.7.1-743/Contents/phenix-1.7.1-743/cctbx_project/mmtbx/model_statistics.py", line 38, in __init__
    compute_gradients = True)

  File "/Applications/PHENIX-1.7.1-743/Contents/phenix-1.7.1-743/cctbx_project/mmtbx/restraints.py", line 66, in energies_sites
    normalization=False)

  File "/Applications/PHENIX-1.7.1-743/Contents/phenix-1.7.1-743/cctbx_project/mmtbx/ncs/restraints.py", line 686, in energies_sites
    self.compute_operators(sites_cart=sites_cart)

  File "/Applications/PHENIX-1.7.1-743/Contents/phenix-1.7.1-743/cctbx_project/mmtbx/ncs/restraints.py", line 679, in compute_operators
    self.operators.append(group.operators(sites_cart=sites_cart))

  File "/Applications/PHENIX-1.7.1-743/Contents/phenix-1.7.1-743/cctbx_project/mmtbx/ncs/restraints.py", line 336, in operators
    return _operators(group=self, sites_cart=sites_cart)

  File "/Applications/PHENIX-1.7.1-743/Contents/phenix-1.7.1-743/cctbx_project/mmtbx/ncs/restraints.py", line 442, in __init__
    other_sites=sites_cart.select(pair[1]))

  File "/Applications/PHENIX-1.7.1-743/Contents/phenix-1.7.1-743/cctbx_project/scitbx/math/superpose.py", line 58, in __init__
    self.reference_shift = reference_sites.mean()



Platform info:
__FILE__ = /net/patchnose/scratch1/phenix/phenix-1.7.1-743/cctbx_project/boost_adaptbx/meta_ext.cpp
__DATE__ = Apr 28 2011
__TIME__ = 02:15:10
__i386__
__APPLE_CC__ = 5367
__GNUC__ = 4
__GNUC_MINOR__ = 0
__GNUC_PATCHLEVEL__ = 1
boost::python::cxxabi_cxa_demangle_is_broken(): false
__GXX_WEAK__ = 1
__VERSION__ = 4.0.1 (Apple Computer, Inc. build 5367)
FE_INEXACT = 32
FE_DIVBYZERO = 4
FE_UNDERFLOW = 16
FE_OVERFLOW = 8
FE_INVALID = 1
FE_ALL_EXCEPT = 61
__SSE2__ = 1
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) = 16
sizeof(boost::int32_t) = 4
sizeof(boost::uint32_t) = 4
sizeof(wchar_t) = 4
__PTRDIFF_TYPE__
Py_USING_UNICODE
sizeof(PY_UNICODE_TYPE) = 2
BOOST_ADAPTBX_TYPE_ID_SIZE_T_EQ_UNSIGNED_LONG
os.name<http://os.name>: posix
sys.platform: darwin
sys.byteorder: little
platform.platform(): Darwin-10.7.4-x86_64-i386-32bit
platform.architecture(): ('32bit', '')
floating_point_exceptions.division_by_zero_trapped: False
floating_point_exceptions.invalid_trapped: False
floating_point_exceptions.overflow_trapped: False
number of processors: 4
Memory total:  4,294,967,296
Memory free:         unknown
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 = √Ö

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