Hi all,<div><br></div><div>I've been trying to refine a structure with anomalous data with anomalous scattering factors. After some refinements without anomalous scattering factor refinement, I used the data.mtz file and original reflection file in reflection file editor to get the anomalous data merged with Rfree flags. When I tried to use this file with a pdb file (deleted hexadigest remark) and a cif file for ligands, the refinement ends with the following error at the end of the 3rd refinement cycle (I have only 3 cycles for a refinement).</div>
<div><br></div><div>I was able to run a similar refinement with anomalous scattering factors for another structure without a problem. One difference in this structure is that this has NCS and the previous one didn't. I am using dev-1243 GUI.</div>
<div><br></div><div>
<p class="MsoNormal"><span style="font-family:Courier">RuntimeError : scitbx array_family range error</span></p>
<p class="MsoNormal"><span style="font-family:Courier">Traceback:</span></p>
<p class="MsoNormal"><span style="font-family:Courier">� File
"/Applications/PHENIX-dev-1243/Contents/phenix-dev-1243/cctbx_project/libtbx/thread_utils.py",
line 234, in run</span></p>
<p class="MsoNormal"><span style="font-family:Courier">���
return_value = self._target(self._args, self._kwargs, self._c)</span></p>
<p class="MsoNormal"><span style="font-family:Courier">�</span></p>
<p class="MsoNormal"><span style="font-family:Courier">� File
"/Applications/PHENIX-dev-1243/Contents/phenix-dev-1243/cctbx_project/libtbx/runtime_utils.py",
line 87, in __call__</span></p>
<p class="MsoNormal"><span style="font-family:Courier">��� result
= self.target()</span></p>
<p class="MsoNormal"><span style="font-family:Courier">�</span></p>
<p class="MsoNormal"><span style="font-family:Courier">� File
"/Applications/PHENIX-dev-1243/Contents/phenix-dev-1243/cctbx_project/libtbx/runtime_utils.py",
line 66, in __call__</span></p>
<p class="MsoNormal"><span style="font-family:Courier">��� result
= self.run()</span></p>
<p class="MsoNormal"><span style="font-family:Courier">�</span></p>
<p class="MsoNormal"><span style="font-family:Courier">� File
"/Applications/PHENIX-dev-1243/Contents/phenix-dev-1243/phenix/phenix/refinement/runtime.py",
line 69, in run</span></p>
<p class="MsoNormal"><span style="font-family:Courier">���
refine_object = self._run(args, callback)</span></p>
<p class="MsoNormal"><span style="font-family:Courier">�</span></p>
<p class="MsoNormal"><span style="font-family:Courier">� File
"/Applications/PHENIX-dev-1243/Contents/phenix-dev-1243/phenix/phenix/refinement/runtime.py",
line 85, in _run</span></p>
<p class="MsoNormal"><span style="font-family:Courier">���
call_back_handler=callback)</span></p>
<p class="MsoNormal"><span style="font-family:Courier">�</span></p>
<p class="MsoNormal"><span style="font-family:Courier">� File
"/Applications/PHENIX-dev-1243/Contents/phenix-dev-1243/phenix/phenix/refinement/command_line.py",
line 169, in run</span></p>
<p class="MsoNormal"><span style="font-family:Courier">���
map_manger.write_files()</span></p>
<p class="MsoNormal"><span style="font-family:Courier">�</span></p>
<p class="MsoNormal"><span style="font-family:Courier">� File
"/Applications/PHENIX-dev-1243/Contents/phenix-dev-1243/phenix/phenix/refinement/driver.py",
line 1735, in write_files</span></p>
<p class="MsoNormal"><span style="font-family:Courier">���
map_coeff_dataset=self.write_mtz_file(),</span></p>
<p class="MsoNormal"><span style="font-family:Courier">�</span></p>
<p class="MsoNormal"><span style="font-family:Courier">� File
"/Applications/PHENIX-dev-1243/Contents/phenix-dev-1243/phenix/phenix/refinement/driver.py",
line 1724, in write_mtz_file</span></p>
<p class="MsoNormal"><span style="font-family:Courier">���
pdb_hierarchy=self.refine_object.model.pdb_hierarchy())</span></p>
<p class="MsoNormal"><span style="font-family:Courier">�</span></p>
<p class="MsoNormal"><span style="font-family:Courier">� File
"/Applications/PHENIX-dev-1243/Contents/phenix-dev-1243/cctbx_project/mmtbx/maps/__init__.py",
line 500, in __init__</span></p>
<p class="MsoNormal"><span style="font-family:Courier">���
pdb_hierarchy = pdb_hierarchy)</span></p>
<p class="MsoNormal"><span style="font-family:Courier">�</span></p>
<p class="MsoNormal"><span style="font-family:Courier">� File
"/Applications/PHENIX-dev-1243/Contents/phenix-dev-1243/cctbx_project/mmtbx/maps/__init__.py",
line 428, in map_coefficients_from_fmodel</span></p>
<p class="MsoNormal"><span style="font-family:Courier">���
sharp����� =
params.sharpening).map_coeffs</span></p>
<p class="MsoNormal"><span style="font-family:Courier">�</span></p>
<p class="MsoNormal"><span style="font-family:Courier">� File
"/Applications/PHENIX-dev-1243/Contents/phenix-dev-1243/cctbx_project/mmtbx/map_tools.py",
line 55, in __init__</span></p>
<p class="MsoNormal"><span style="font-family:Courier">��� data =
self.map_coeffs.data()*scale)</span></p>
<p class="MsoNormal"><span style="font-family:Courier">�</span></p>
<p class="MsoNormal">�</p><p class="MsoNormal">Thanks in advance for any help</p><p class="MsoNormal"><br></p><p class="MsoNormal">Subhani</p>
</div>