[phenixbb] AssertionError in twin refinement...

Francis E Reyes Francis.Reyes at Colorado.EDU
Wed Mar 25 13:21:54 PDT 2009



====================== 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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