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: 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