[phenixbb] NCS error in Phenix 1.7.1-743

Fri Jun 24 07:36:17 PDT 2011

We've seen this before - it seems to happen only with certain
structures.  When I tried debugging this for someone else, I found
that the newer code didn't crash like this (but I could reproduce it
in 1.7.1).  Could you please try updating to a recent nightly build
and see if that fixes the problem?

-Nat

On Fri, Jun 24, 2011 at 1:07 AM, Ngan Nguyen Bich
<ngan.nguyenbich at student.kuleuven.be> wrote:
> 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
>
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