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 [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb--------------------------------------------- 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 [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb