[phenixbb] 'ordered solvent' switch error (AssertionError)

Jonathan Elegheert jonathan.elegheert at ugent.be
Fri Aug 22 15:11:34 PDT 2008


Dear Phenix developers,

since downloading the latest CCI Apps software release version 
(2008_08_09_0053), I keep running into this same error (AssertionError) 
when turning on the 'ordered solvent' switch in phenix.refine. I did not 
encounter this error with the 'release candidate 2' version I was 
running previously.

Platform: RHEL4 with the Red Hat 8.0 or the Red Hat WS 3 (x86_64) binary 
bundles.

Many thanks in advance for your help.

Jonathan Elegheert, PhD student
Ghent University

================== ordered solvent: location/analysis/update 
==================

Start model:
  number           = 359
  b_iso_min        = 7.13    (limit = 1.00)
  b_iso_max        = 56.80   (limit = 50.00)
  b_iso_mean       = 27.85
  anisotropy_min   = 1.00    (limit = 0.10)
  occupancy_min    = 1.00    (limit = 1.00)
  occupancy_max    = 1.00    (limit = 1.00)
  dist_sol_mol_min = 1.92    (limit = 1.80)
  dist_sol_mol_max = 4.46    (limit = 6.00)
Filtered:
  number           = 324
  b_iso_min        = 7.13    (limit = 1.00)
  b_iso_max        = 49.84   (limit = 50.00)
  b_iso_mean       = 26.59
  anisotropy_min   = 1.00    (limit = 0.10)
  occupancy_min    = 1.00    (limit = 1.00)
  occupancy_max    = 1.00    (limit = 1.00)
  dist_sol_mol_min = 2.05    (limit = 1.80)
  dist_sol_mol_max = 4.18    (limit = 6.00)
Traceback (most recent call last):
  File 
"/usr/local/PHENIX/cci_apps_sources/phenix/phenix/command_line/refine.py", 
line 5, in <module>
    command_line.run(command_name="phenix.refine", args=sys.argv[1:])
  File 
"/usr/local/PHENIX/cci_apps_sources/phenix/phenix/refinement/command_line.py", 
line 89, in run
    call_back_after_monitor_collect=call_back_after_monitor_collect)
  File 
"/usr/local/PHENIX/cci_apps_sources/phenix/phenix/refinement/driver.py", 
line 1081, in run
    call_back_after_monitor_collect = call_back_after_monitor_collect)
  File 
"/usr/local/PHENIX/cci_apps_sources/phenix/phenix/refinement/strategies.py", 
line 364, in refinement_machine
    log               = log)
  File 
"/usr/local/PHENIX/cci_apps_sources/mmtbx/mmtbx/solvent/ordered_solvent.py", 
line 159, in __init__
    use_kick_map = self.params.use_kick_maps).peaks_mapped()
  File 
"/usr/local/PHENIX/cci_apps_sources/mmtbx/mmtbx/solvent/ordered_solvent.py", 
line 332, in find_peaks
    log             = self.log)
  File "/usr/local/PHENIX/cci_apps_sources/mmtbx/mmtbx/find_peaks.py", 
line 85, in __init__
    symmetry_flags    = maptbx.use_space_group_symmetry)
  File 
"/usr/local/PHENIX/cci_apps_sources/mmtbx/mmtbx/twinning/twin_f_model.py", 
line 2244, in electron_density_map
    "m_gradient")
AssertionError



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