[phenixbb] crash during refinement with twinned data

Scott White s.a.white at bham.ac.uk
Mon Sep 10 05:48:43 PDT 2007

Dear PhenixBB,

I'm trying to refine a structure against potentially twinned data. I
got the twin law from xtriage. phenix.refine starts, and at some point
crashes with the messages below. Refinement proceeds to the end if I
don't include twinning.

Any suggestions?

Thanks, Scott

Traceback (most recent call last):
 File "/software/phenix-1.3b/phenix/phenix/command_line/refine.py",
line 5, in <module>
   command_line.run(command_name="phenix.refine", args=sys.argv[1:])
 File "/software/phenix-1.3b/phenix/phenix/refinement/command_line.py",
line 81, in run
 File "/software/phenix-1.3b/phenix/phenix/refinement/driver.py",
line 1325, in run
   log                     = log)
 File "/software/phenix-1.3b/phenix/phenix/refinement/strategies.py",
line 559, in refinement_machine
   log                     = log)
 File "/software/phenix-1.3b/mmtbx/mmtbx/refinement/rigid_body.py",
line 347, in __init__
   fmodel_copy = fmodel.resolution_filter(d_min = res)
 File "/software/phenix-1.3b/mmtbx/mmtbx/twinning/twin_f_model.py",
line 1042, in resolution_filter
   sf_and_grads_accuracy_params = dc.sfg_params
 File "/software/phenix-1.3b/mmtbx/mmtbx/twinning/twin_f_model.py",
line 890, in __init__
   u_part=self.scaling_parameters.u_part )
RuntimeError: cctbx Internal Error:
CCTBX_ASSERT((f_mask.size() == 0) || (hkl.size() == f_mask.size()))

  Dr Scott A. White
  Protein Crystallography Group
  School of Biosciences
  University of Birmingham
  B15 2TT
  E: s.a.white at bham.ac.uk
  T: +44-(0)121-414-7534
  F: +44-(0)121-414-5925
  W: http://www.bip.bham.ac.uk/cryst

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