[phenixbb] error with phenix.refinine

Maxime Cuypers maximecuypers at gmail.com
Sun Nov 8 12:09:32 PST 2015


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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