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

Peter Zwart PHZwart at lbl.gov
Fri Aug 22 15:25:20 PDT 2008


My bad again (i think)

I'll have a look.

P


2008/8/22 Jonathan Elegheert <jonathan.elegheert at ugent.be>:
> 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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> phenixbb at phenix-online.org
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>



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P.H. Zwart
Beamline Scientist
Berkeley Center for Structural Biology
Lawrence Berkeley National Laboratories
1 Cyclotron Road, Berkeley, CA-94703, USA
Cell: 510 289 9246
BCSB: http://bcsb.als.lbl.gov
PHENIX: http://www.phenix-online.org
CCTBX: http://cctbx.sf.net
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