[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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