[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
>>>
>>> _______________________________________________
>>> phenixbb mailing list
>>> phenixbb at phenix-online.org
>>> http://www.phenix-online.org/mailman/listinfo/phenixbb
>>>
>>>
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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
> phenixbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb
>
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