<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><font class="Apple-style-span" face="Arial">Dear all,</font><div><font class="Apple-style-span" face="Arial"><br></font></div><div><font class="Apple-style-span" face="Arial">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</font></div><div><font class="Apple-style-span" face="Arial"><br></font></div><div><font class="Apple-style-span" face="Arial">In the old computer I set two NCS restraints groups as:</font></div><div><font class="Apple-style-span" face="Arial">First group:</font></div><div><font class="Apple-style-span" face="Arial">Reference group: </font><span class="Apple-style-span" style="font-size: 12px; "><font class="Apple-style-span" face="Arial">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)</font></span></div><div><span class="Apple-style-span" style="font-size: 12px; "><font class="Apple-style-span" face="Arial">Second group:</font></span></div><div><span class="Apple-style-span" style="font-size: 12px; "><font class="Apple-style-span" face="Arial">Reference group: </font></span><span class="Apple-style-span" style="font-size: 12px; "><font class="Apple-style-span" face="Arial">chain A <font class="Apple-style-span" color="#2F4FF6">and backbone</font> and resid 3:217 and not (resid 63 or resid 133 or resid 135 or resid 184)</font></span></div><div><span class="Apple-style-span" style="font-size: 12px; "><font class="Apple-style-span" face="Arial">And the refine_phenix run well in the old computer, but the new laptop with t</font></span><span class="Apple-style-span" style="font-family: Arial; font-size: 12px; ">he error in the end of this letter.</span></div><div><span class="Apple-style-span" style="font-size: 12px; "><font class="Apple-style-span" face="Arial">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?</font></span></div><div><font class="Apple-style-span" face="Arial"><br></font></div><div><font class="Apple-style-span" face="Arial">Thank you in advance.</font></div><div><font class="Apple-style-span" face="Arial">Ngan</font></div><div><span class="Apple-style-span" style="font-family: Monaco; font-size: 12px; "><div><font class="Apple-style-span" face="Arial"><br></font></div><div><font class="Apple-style-span" face="Arial">RuntimeError : mean() argument is an empty array</font></div><div><font class="Apple-style-span" face="Arial">Traceback:</font></div><div><font class="Apple-style-span" face="Arial"> File "/Applications/PHENIX-1.7.1-743/Contents/phenix-1.7.1-743/cctbx_project/libtbx/thread_utils.py", line 223, in run</font></div><div><font class="Apple-style-span" face="Arial"> return_value = self._target(self._args, self._kwargs, self._c)</font></div><div><font class="Apple-style-span" face="Arial"><br></font></div><div><font class="Apple-style-span" face="Arial"> File "/Applications/PHENIX-1.7.1-743/Contents/phenix-1.7.1-743/cctbx_project/libtbx/runtime_utils.py", line 58, in __call__</font></div><div><font class="Apple-style-span" face="Arial"> result = self.target()</font></div><div><font class="Apple-style-span" face="Arial"><br></font></div><div><font class="Apple-style-span" face="Arial"> File "/Applications/PHENIX-1.7.1-743/Contents/phenix-1.7.1-743/phenix/phenix/refinement/runtime.py", line 68, in __call__</font></div><div><font class="Apple-style-span" face="Arial"> call_back_handler=callback)</font></div><div><font class="Apple-style-span" face="Arial"><br></font></div><div><font class="Apple-style-span" face="Arial"> File "/Applications/PHENIX-1.7.1-743/Contents/phenix-1.7.1-743/phenix/phenix/refinement/command_line.py", line 89, in run</font></div><div><font class="Apple-style-span" face="Arial"> call_back_handler=call_back_handler)</font></div><div><font class="Apple-style-span" face="Arial"><br></font></div><div><font class="Apple-style-span" face="Arial"> File "/Applications/PHENIX-1.7.1-743/Contents/phenix-1.7.1-743/phenix/phenix/refinement/driver.py", line 1278, in run</font></div><div><font class="Apple-style-span" face="Arial"> reference_model_manager = self.reference_model_manager)</font></div><div><font class="Apple-style-span" face="Arial"><br></font></div><div><font class="Apple-style-span" face="Arial"> File "/Applications/PHENIX-1.7.1-743/Contents/phenix-1.7.1-743/phenix/phenix/refinement/strategies.py", line 322, in refinement_machine</font></div><div><font class="Apple-style-span" face="Arial"> monitors.collect(step = "0 :", model = model, fmodels = fmodels)</font></div><div><font class="Apple-style-span" face="Arial"><br></font></div><div><font class="Apple-style-span" face="Arial"> File "/Applications/PHENIX-1.7.1-743/Contents/phenix-1.7.1-743/cctbx_project/mmtbx/refinement/__init__.py", line 51, in collect</font></div><div><font class="Apple-style-span" face="Arial"> rigid_body_shift_accumulator = rigid_body_shift_accumulator)</font></div><div><font class="Apple-style-span" face="Arial"><br></font></div><div><font class="Apple-style-span" face="Arial"> File "/Applications/PHENIX-1.7.1-743/Contents/phenix-1.7.1-743/cctbx_project/mmtbx/refinement/print_statistics.py", line 263, in collect</font></div><div><font class="Apple-style-span" face="Arial"> ignore_side_chain = True,</font></div><div><font class="Apple-style-span" face="Arial"><br></font></div><div><font class="Apple-style-span" face="Arial"> File "/Applications/PHENIX-1.7.1-743/Contents/phenix-1.7.1-743/cctbx_project/mmtbx/model.py", line 971, in geometry_statistics</font></div><div><font class="Apple-style-span" face="Arial"> restraints_manager = self.restraints_manager)</font></div><div><font class="Apple-style-span" face="Arial"><br></font></div><div><font class="Apple-style-span" face="Arial"> File "/Applications/PHENIX-1.7.1-743/Contents/phenix-1.7.1-743/cctbx_project/mmtbx/model_statistics.py", line 38, in __init__</font></div><div><font class="Apple-style-span" face="Arial"> compute_gradients = True)</font></div><div><font class="Apple-style-span" face="Arial"><br></font></div><div><font class="Apple-style-span" face="Arial"> File "/Applications/PHENIX-1.7.1-743/Contents/phenix-1.7.1-743/cctbx_project/mmtbx/restraints.py", line 66, in energies_sites</font></div><div><font class="Apple-style-span" face="Arial"> normalization=False)</font></div><div><font class="Apple-style-span" face="Arial"><br></font></div><div><font class="Apple-style-span" face="Arial"> File "/Applications/PHENIX-1.7.1-743/Contents/phenix-1.7.1-743/cctbx_project/mmtbx/ncs/restraints.py", line 686, in energies_sites</font></div><div><font class="Apple-style-span" face="Arial"> self.compute_operators(sites_cart=sites_cart)</font></div><div><font class="Apple-style-span" face="Arial"><br></font></div><div><font class="Apple-style-span" face="Arial"> File "/Applications/PHENIX-1.7.1-743/Contents/phenix-1.7.1-743/cctbx_project/mmtbx/ncs/restraints.py", line 679, in compute_operators</font></div><div><font class="Apple-style-span" face="Arial"> self.operators.append(group.operators(sites_cart=sites_cart))</font></div><div><font class="Apple-style-span" face="Arial"><br></font></div><div><font class="Apple-style-span" face="Arial"> File "/Applications/PHENIX-1.7.1-743/Contents/phenix-1.7.1-743/cctbx_project/mmtbx/ncs/restraints.py", line 336, in operators</font></div><div><font class="Apple-style-span" face="Arial"> return _operators(group=self, sites_cart=sites_cart)</font></div><div><font class="Apple-style-span" face="Arial"><br></font></div><div><font class="Apple-style-span" face="Arial"> File "/Applications/PHENIX-1.7.1-743/Contents/phenix-1.7.1-743/cctbx_project/mmtbx/ncs/restraints.py", line 442, in __init__</font></div><div><font class="Apple-style-span" face="Arial"> other_sites=sites_cart.select(pair[1]))</font></div><div><font class="Apple-style-span" face="Arial"><br></font></div><div><font class="Apple-style-span" face="Arial"> File "/Applications/PHENIX-1.7.1-743/Contents/phenix-1.7.1-743/cctbx_project/scitbx/math/superpose.py", line 58, in __init__</font></div><div><font class="Apple-style-span" face="Arial"> self.reference_shift = reference_sites.mean()</font></div><div><font class="Apple-style-span" face="Arial"><br></font></div><div><font class="Apple-style-span" face="Arial"><br></font></div><div><font class="Apple-style-span" face="Arial"><br></font></div><div><font class="Apple-style-span" face="Arial">Platform info:</font></div><div><font class="Apple-style-span" face="Arial">__FILE__ = /net/patchnose/scratch1/phenix/phenix-1.7.1-743/cctbx_project/boost_adaptbx/meta_ext.cpp</font></div><div><font class="Apple-style-span" face="Arial">__DATE__ = Apr 28 2011</font></div><div><font class="Apple-style-span" face="Arial">__TIME__ = 02:15:10</font></div><div><font class="Apple-style-span" face="Arial">__i386__</font></div><div><font class="Apple-style-span" face="Arial">__APPLE_CC__ = 5367</font></div><div><font class="Apple-style-span" face="Arial">__GNUC__ = 4</font></div><div><font class="Apple-style-span" face="Arial">__GNUC_MINOR__ = 0</font></div><div><font class="Apple-style-span" face="Arial">__GNUC_PATCHLEVEL__ = 1</font></div><div><font class="Apple-style-span" face="Arial">boost::python::cxxabi_cxa_demangle_is_broken(): false</font></div><div><font class="Apple-style-span" face="Arial">__GXX_WEAK__ = 1</font></div><div><font class="Apple-style-span" face="Arial">__VERSION__ = 4.0.1 (Apple Computer, Inc. build 5367)</font></div><div><font class="Apple-style-span" face="Arial">FE_INEXACT = 32</font></div><div><font class="Apple-style-span" face="Arial">FE_DIVBYZERO = 4</font></div><div><font class="Apple-style-span" face="Arial">FE_UNDERFLOW = 16</font></div><div><font class="Apple-style-span" face="Arial">FE_OVERFLOW = 8</font></div><div><font class="Apple-style-span" face="Arial">FE_INVALID = 1</font></div><div><font class="Apple-style-span" face="Arial">FE_ALL_EXCEPT = 61</font></div><div><font class="Apple-style-span" face="Arial">__SSE2__ = 1</font></div><div><font class="Apple-style-span" face="Arial">BOOST_LIB_VERSION = 1_47</font></div><div><font class="Apple-style-span" face="Arial">PY_VERSION = 2.7.1</font></div><div><font class="Apple-style-span" face="Arial">PYTHON_API_VERSION = 1013</font></div><div><font class="Apple-style-span" face="Arial">sizeof(bool) = 1</font></div><div><font class="Apple-style-span" face="Arial">sizeof(short) = 2</font></div><div><font class="Apple-style-span" face="Arial">sizeof(int) = 4</font></div><div><font class="Apple-style-span" face="Arial">sizeof(long) = 4</font></div><div><font class="Apple-style-span" face="Arial">sizeof(std::size_t) = 4</font></div><div><font class="Apple-style-span" face="Arial">sizeof(void*) = 4</font></div><div><font class="Apple-style-span" face="Arial">sizeof(long long) = 8</font></div><div><font class="Apple-style-span" face="Arial">sizeof(float) = 4</font></div><div><font class="Apple-style-span" face="Arial">sizeof(double) = 8</font></div><div><font class="Apple-style-span" face="Arial">sizeof(long double) = 16</font></div><div><font class="Apple-style-span" face="Arial">sizeof(boost::int32_t) = 4</font></div><div><font class="Apple-style-span" face="Arial">sizeof(boost::uint32_t) = 4</font></div><div><font class="Apple-style-span" face="Arial">sizeof(wchar_t) = 4</font></div><div><font class="Apple-style-span" face="Arial">__PTRDIFF_TYPE__</font></div><div><font class="Apple-style-span" face="Arial">Py_USING_UNICODE</font></div><div><font class="Apple-style-span" face="Arial">sizeof(PY_UNICODE_TYPE) = 2</font></div><div><font class="Apple-style-span" face="Arial">BOOST_ADAPTBX_TYPE_ID_SIZE_T_EQ_UNSIGNED_LONG</font></div><div><font class="Apple-style-span" face="Arial"><a href="http://os.name">os.name</a>: posix</font></div><div><font class="Apple-style-span" face="Arial">sys.platform: darwin</font></div><div><font class="Apple-style-span" face="Arial">sys.byteorder: little</font></div><div><font class="Apple-style-span" face="Arial">platform.platform(): Darwin-10.7.4-x86_64-i386-32bit</font></div><div><font class="Apple-style-span" face="Arial">platform.architecture(): ('32bit', '')</font></div><div><font class="Apple-style-span" face="Arial">floating_point_exceptions.division_by_zero_trapped: False</font></div><div><font class="Apple-style-span" face="Arial">floating_point_exceptions.invalid_trapped: False</font></div><div><font class="Apple-style-span" face="Arial">floating_point_exceptions.overflow_trapped: False</font></div><div><font class="Apple-style-span" face="Arial">number of processors: 4</font></div><div><font class="Apple-style-span" face="Arial">Memory total: 4,294,967,296</font></div><div><font class="Apple-style-span" face="Arial">Memory free: unknown</font></div><div><font class="Apple-style-span" face="Arial">import thread: OK</font></div><div><font class="Apple-style-span" face="Arial">"hello" = ['h', 'e', 'l', 'l', 'o']</font></div><div><font class="Apple-style-span" face="Arial">u"hello" = ['h', '\x00', 'e', '\x00', 'l', '\x00', 'l', '\x00', 'o', '\x00']</font></div><div><font class="Apple-style-span" face="Arial">u"\u00C5" = ['\xc5', '\x00'] as utf-8 = ['\xc3', '\x85']</font></div><div><font class="Apple-style-span" face="Arial">LATIN CAPITAL LETTER A WITH RING ABOVE = √Ö</font></div><div><br></div></span></div></body></html>