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Hi Maxime,<br>
<br>
I'm sorry for the problem! I'm keen to address it asap. For that
could you please send me all inputs (off list, to me directly) so
that I can reproduce this error myself and then fix it?<br>
<br>
Thanks,<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 11/8/15 12:09, Maxime Cuypers wrote:<br>
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<div>hi,<br>
<br>
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i have the following error refining a neutron structure
(no xrays data) with the latest builds (dev and
official):<br>
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it used to work perfectly and now it says:<br>
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tried many things with my pdb yet to no avail. even archived
runs do not work anymore.<br>
<br>
====================== ADP refinement (reciprocal space)
======================<br>
<br>
<br>
���������������� ----------Individual ADP
refinement----------���������������� <br>
<br>
��� R-FACTORS����� <Bi-Bj>� <B>�� WEIGHT������
TARGETS<br>
�work� free� delta�������������������������� data restr<br>
19.38 23.49�� 4.11� 1.665� 13.405 32.138��� 0.039<br>
Traceback (most recent call last):<br>
� File
"/usr/local/phenix-1.10.1-2155/build/../modules/phenix/phenix/command_line/refine.py",
line 11, in <module><br>
��� command_line.run(command_name="phenix.refine",
args=sys.argv[1:])<br>
� File
"/usr/local/phenix-1.10.1-2155/modules/phenix/phenix/refinement/command_line.py",
line 162, in run<br>
��� call_back_handler=call_back_handler)<br>
� File
"/usr/local/phenix-1.10.1-2155/modules/phenix/phenix/refinement/driver.py",
line 1532, in run<br>
��� call_back_handler������ = call_back_handler).result<br>
� File
"/usr/local/phenix-1.10.1-2155/modules/phenix/phenix/refinement/strategies.py",
line 201, in __init__<br>
��� ion_placement_manager = ion_placement_manager)<br>
� File
"/usr/local/phenix-1.10.1-2155/modules/phenix/phenix/refinement/macro_cycle.py",
line 117, in __init__<br>
��� self.call(self.adp,����� "ADP refinement (reciprocal
space)")<br>
� File
"/usr/local/phenix-1.10.1-2155/modules/phenix/phenix/refinement/macro_cycle.py",
line 143, in call<br>
��� func(prefix = prefix)<br>
� File
"/usr/local/phenix-1.10.1-2155/modules/phenix/phenix/refinement/macro_cycle.py",
line 396, in adp<br>
��� log��������������������� = self.log)<br>
� File
"/usr/local/phenix-1.10.1-2155/modules/phenix/phenix/refinement/adp.py",
line 62, in run<br>
��� h_params�������������� = h_params)<br>
� File
"/usr/local/phenix-1.10.1-2155/modules/cctbx_project/mmtbx/refinement/adp_refinement.py",
line 232, in __init__<br>
��� nproc���������������� = nproc)<br>
� File
"/usr/local/phenix-1.10.1-2155/modules/cctbx_project/mmtbx/refinement/adp_refinement.py",
line 337, in __init__<br>
��� result = self.try_weight(weight, print_stats=True)<br>
� File
"/usr/local/phenix-1.10.1-2155/modules/cctbx_project/mmtbx/refinement/adp_refinement.py",
line 427, in try_weight<br>
��� minimized = self.minimize()<br>
� File
"/usr/local/phenix-1.10.1-2155/modules/cctbx_project/mmtbx/refinement/adp_refinement.py",
line 496, in minimize<br>
��� self.model.set_refine_individual_adp()<br>
� File
"/usr/local/phenix-1.10.1-2155/modules/cctbx_project/mmtbx/model.py",
line 1523, in set_refine_individual_adp<br>
��� iselection = selection_iso.iselection())<br>
RuntimeError: cctbx Internal Error:
/home/builder/slave/phenix-nightly-intel-linux-2_6-x86_64-centos5/modules/cctbx_project/cctbx/xray/scatterer_flags.h(417):
CCTBX_ASSERT(f.use_u_iso()) failure.<br>
<br>
<br>
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any clue what is happening? <br>
<br>
</div>
thank you for your help,<br>
<br>
<div>
<div>Maxime Cuypers<br>
</div>
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