[phenixbb] AssertionError in twin refinement...
Pavel Afonine
PAfonine at lbl.gov
Wed Mar 25 13:26:48 PDT 2009
Hi Francis,
could you try the latest version? I think I this this problem was
reported and fixed sometime ago. Please let us know if you are still
getting this error using the latest version.
Pavel.
On 3/25/09 1:21 PM, Francis E Reyes wrote:
> ====================== bulk solvent modeling and scaling
> ======================
>
> |--(resolution: 2.00 - 23.08 A; n_refl. =
> 24304)------------------------------|
> |
> |
> | r_work= 0.2462 r_free= 0.2706 ksol= 0.32 Bsol= 47.55 scale=
> 1.149 |
> |
> |
> | overall anisotropic scale matrix (Cartesian basis;
> B11,B22,B33,B12,B13,B23):|
> | (-2.11,5.80,-3.69,0.00,-0.00,-0.00); trace/3=
> -0.00 |
> |
> |
> | maximum likelihood estimate for coordinate error: None
> A |
> | x-ray target function (twin_lsq_f) for work reflections:
> 0.346916 |
> | twin fraction: 0.03 twin operator: k,h,-
> l |
> |
> -----------------------------------------------------------------------------|
>
> ================== ordered solvent: location/analysis/update
> ==================
>
> Start model:
> number = 165
> b_iso_min = 37.62 (limit = 1.00)
> b_iso_max = 70.26 (limit = 50.00)
> b_iso_mean = 49.33
> 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 = 2.45 (limit = 1.80)
> dist_sol_mol_max = 4.94 (limit = 6.00)
> Filtered:
> number = 71
> b_iso_min = 37.71 (limit = 1.00)
> b_iso_max = 49.89 (limit = 50.00)
> b_iso_mean = 45.14
> 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 = 2.45 (limit = 1.80)
> dist_sol_mol_max = 3.99 (limit = 6.00)
> Traceback (most recent call last):
> File "/usr/local/phenix-1.3-final/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-1.3-final/phenix/phenix/refinement/
> command_line.py", line 89, in run
> call_back_after_monitor_collect=call_back_after_monitor_collect)
> File "/usr/local/phenix-1.3-final/phenix/phenix/refinement/
> driver.py", line 1081, in run
> call_back_after_monitor_collect = call_back_after_monitor_collect)
> File "/usr/local/phenix-1.3-final/phenix/phenix/refinement/
> strategies.py", line 364, in refinement_machine
> log = log)
> File "/usr/local/phenix-1.3-final/mmtbx/mmtbx/solvent/
> ordered_solvent.py", line 159, in __init__
> use_kick_map = self.params.use_kick_maps).peaks_mapped()
> File "/usr/local/phenix-1.3-final/mmtbx/mmtbx/solvent/
> ordered_solvent.py", line 332, in find_peaks
> log = self.log)
> File "/usr/local/phenix-1.3-final/mmtbx/mmtbx/find_peaks.py", line
> 85, in __init__
> symmetry_flags = maptbx.use_space_group_symmetry)
> File "/usr/local/phenix-1.3-final/mmtbx/mmtbx/twinning/
> twin_f_model.py", line 2244, in electron_density_map
> "m_gradient")
> AssertionError
>
>
>
> phenix version is 1.3 final.
>
> Ideas?
>
> thanks!
>
> FR
>
> ---------------------------------------------
> Francis Reyes M.Sc.
> 215 UCB
> University of Colorado at Boulder
>
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>
> 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
>
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