[phenixbb] AssertionError in twin refinement...

Pavel Afonine PAfonine at lbl.gov
Wed Mar 25 14:00:04 PDT 2009


Could you please send me the exact command you use (including the 
content of parameter files)? Then I will try to reproduce this failure 
myself... No need for the mode/data at this point.

Thanks!
Pavel.


On 3/25/09 1:51 PM, Francis E Reyes wrote:
> Pavel
>
> Seems to occur in 1.4-3 as well.
>
> Traceback (most recent call last):
>    File "/usr/local/phenix-1.4-3/phenix/phenix/command_line/ 
> refine.py", line 9, in <module>
>      command_line.run(command_name="phenix.refine", args=sys.argv[1:])
>    File "/usr/local/phenix-1.4-3/phenix/phenix/refinement/ 
> command_line.py", line 89, in run
>      call_back_after_monitor_collect=call_back_after_monitor_collect)
>    File "/usr/local/phenix-1.4-3/phenix/phenix/refinement/driver.py",  
> line 1098, in run
>      call_back_after_monitor_collect = call_back_after_monitor_collect)
>    File "/usr/local/phenix-1.4-3/phenix/phenix/refinement/ 
> strategies.py", line 363, in refinement_machine
>      log               = log)
>    File "/usr/local/phenix-1.4-3/mmtbx/solvent/ordered_solvent.py",  
> line 159, in __init__
>      use_kick_map = self.params.use_kick_maps).peaks_mapped()
>    File "/usr/local/phenix-1.4-3/mmtbx/solvent/ordered_solvent.py",  
> line 334, in find_peaks
>      log             = self.log)
>    File "/usr/local/phenix-1.4-3/mmtbx/find_peaks.py", line 84, in  
> __init__
>      map_type          = self.map_type)
>    File "/usr/local/phenix-1.4-3/mmtbx/twinning/twin_f_model.py", line  
> 2344, in fft_map
>      w2                = w2)
>    File "/usr/local/phenix-1.4-3/mmtbx/twinning/twin_f_model.py", line  
> 2213, in map_coefficients
>      "m_gradient"
> AssertionError
>
>
>
> FR
>
>
> On Mar 25, 2009, at 2:26 PM, Pavel Afonine wrote:
>
>   
>> 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
>>>
>>> gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D
>>>
>>> 8AE2 F2F4 90F7 9640 28BC  686F 78FD 6669 67BA 8D5D
>>>
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>>> phenixbb mailing list
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>>>
>>>       
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>>     
>
> ---------------------------------------------
> Francis Reyes M.Sc.
> 215 UCB
> University of Colorado at Boulder
>
> gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D
>
> 8AE2 F2F4 90F7 9640 28BC  686F 78FD 6669 67BA 8D5D
>
> _______________________________________________
> phenixbb mailing list
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> http://www.phenix-online.org/mailman/listinfo/phenixbb
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