Hi Maxime, 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? Thanks, Pavel On 11/8/15 12:09, Maxime Cuypers wrote:
hi,
i have the following error refining a neutron structure (no xrays data) with the latest builds (dev and official): it used to work perfectly and now it says: tried many things with my pdb yet to no avail. even archived runs do not work anymore.
====================== ADP refinement (reciprocal space) ======================
----------Individual ADP refinement----------
R-FACTORS <Bi-Bj> <B> WEIGHT TARGETS work free delta data restr 19.38 23.49 4.11 1.665 13.405 32.138 0.039 Traceback (most recent call last): File "/usr/local/phenix-1.10.1-2155/build/../modules/phenix/phenix/command_line/refine.py", line 11, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix-1.10.1-2155/modules/phenix/phenix/refinement/command_line.py", line 162, in run call_back_handler=call_back_handler) File "/usr/local/phenix-1.10.1-2155/modules/phenix/phenix/refinement/driver.py", line 1532, in run call_back_handler = call_back_handler).result File "/usr/local/phenix-1.10.1-2155/modules/phenix/phenix/refinement/strategies.py", line 201, in __init__ ion_placement_manager = ion_placement_manager) File "/usr/local/phenix-1.10.1-2155/modules/phenix/phenix/refinement/macro_cycle.py", line 117, in __init__ self.call(self.adp, "ADP refinement (reciprocal space)") File "/usr/local/phenix-1.10.1-2155/modules/phenix/phenix/refinement/macro_cycle.py", line 143, in call func(prefix = prefix) File "/usr/local/phenix-1.10.1-2155/modules/phenix/phenix/refinement/macro_cycle.py", line 396, in adp log = self.log) File "/usr/local/phenix-1.10.1-2155/modules/phenix/phenix/refinement/adp.py", line 62, in run h_params = h_params) File "/usr/local/phenix-1.10.1-2155/modules/cctbx_project/mmtbx/refinement/adp_refinement.py", line 232, in __init__ nproc = nproc) File "/usr/local/phenix-1.10.1-2155/modules/cctbx_project/mmtbx/refinement/adp_refinement.py", line 337, in __init__ result = self.try_weight(weight, print_stats=True) File "/usr/local/phenix-1.10.1-2155/modules/cctbx_project/mmtbx/refinement/adp_refinement.py", line 427, in try_weight minimized = self.minimize() File "/usr/local/phenix-1.10.1-2155/modules/cctbx_project/mmtbx/refinement/adp_refinement.py", line 496, in minimize self.model.set_refine_individual_adp() File "/usr/local/phenix-1.10.1-2155/modules/cctbx_project/mmtbx/model.py", line 1523, in set_refine_individual_adp iselection = selection_iso.iselection()) 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.
any clue what is happening?
thank you for your help,
Maxime Cuypers
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