[phenixbb] AssertionError in twin refinement...

[Francis E Reyes]

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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---------------------------------------------
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