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

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--------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder

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Thanks for the files, I will have a look. Pavel. On 3/25/09 2:01 PM, Francis E Reyes wrote:

Command: phenix.refine *004.def --overwrite --unused_ok refinement.input.xray_data.r_free_flags.generate=True

and the def file is enclosed.

I turned off ordered_solvent and it seems to be working OK with the twin refinement (I can actually make it into simulated annealing).

On Mar 25, 2009, at 3:00 PM, Pavel Afonine wrote:

...

--------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder

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Hi Francis, the problem was in this line (and this is really our technical problem and not your fault): primary_map_type = "m*Fobs-D*Fmodel" which is in newer version looks like this: primary_map_type = "mFobs-DFmodel" It would not matter in refinement using non-twinned data (both will be recognized automatically), but in twin refinement phenix.refine uses some different internal routines that are less automated about this. The take-home lesson: it is always the best to use newly generated parameter sets to make sure you are up-to-date with all eventual changes in parameters that might come along with a newer version.

Command: phenix.refine *004.def --overwrite --unused_ok refinement.input.xray_data.r_free_flags.generate=True

Just a couple of comments on the above line: It is a bit dangerous to use "--unused_ok" because it will force phenix.refine to ignore the parameters that it did not recognize and so it will keep going, while you may still be thinking that those parameters are used. So, I wouldn't use this option unless you are very sure. This "refinement.input.xray_data.r_free_flags.generate=True" should be used only once at the very beginning BEFORE any refinement is done, otherwise it will re-create the test set reflections every time you start the refinement therefore making the Rfree statistics invalid. Pavel.