Hi Shi Jiahai, please download and install the latest version from nightly builds: http://www.phenix-online.org/download/ under "Nightly builds (version 1.4-4 and above)" goto "Latest installers", and hopefully the problem will go away. Please let us know if this does not help. Pavel. On 8/4/09 6:47 AM, shi jiahai wrote:
Hi, Dear all,
I am refine a twin dataset with phenix 1.4-3 and CCI (2008_02_08_1610) on a CenOS 5.2 workstation.
When I run refine with twin law or order_solvent alone, the refinement is good. Everything goes smoothly. However if I enable refinement on both twin law and order_solvent, the error comes during the order_solvent refinement as below.
Start model: number = 55 b_iso_min = 5.52 (limit = 1.00) b_iso_max = 60.32 (limit = 60.00) b_iso_mean = 24.19 anisotropy_min = 1.00 (limit = 0.10) occupancy_min = 1.00 (limit = 0.10) occupancy_max = 1.00 (limit = 1.20) dist_sol_mol_min = 2.13 (limit = 1.80) dist_sol_mol_max = 4.38 (limit = 6.00) Traceback (most recent call last): File "/Application/CCI/cci_apps_sources/phenix/phenix/command_line/refine.py", line 5, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/Application/CCI/cci_apps_sources/phenix/phenix/refinement/command_line.py", line 80, in run call_back_after_monitor_collect=call_back_after_monitor_collect) File "/Application/CCI/cci_apps_sources/phenix/phenix/refinement/driver.py", line 1162, in run call_back_after_monitor_collect = call_back_after_monitor_collect) File "/Application/CCI/cci_apps_sources/phenix/phenix/refinement/strategies.py", line 350, in refinement_machine log = log) File "/Application/CCI/cci_apps_sources/mmtbx/mmtbx/solvent/ordered_solvent.py", line 132, in __init__ map_cutoff = self.params.primary_map_cutoff).peaks_mapped() File "/Application/CCI/cci_apps_sources/mmtbx/mmtbx/solvent/ordered_solvent.py", line 324, in find_peaks log = self.log) File "/Application/CCI/cci_apps_sources/mmtbx/mmtbx/find_peaks.py", line 65, in __init__ symmetry_flags = maptbx.use_space_group_symmetry) File "/Application/CCI/cci_apps_sources/mmtbx/mmtbx/twinning/twin_f_model.py", line 2238, in electron_density_map w2 = w2).fft_map( File "/Application/CCI/cci_apps_sources/mmtbx/mmtbx/twinning/twin_f_model.py", line 2126, in map_coefficients "m_gradient" AssertionError
Can anybody help me with this? Thanks a lot in advance!
Best Regards,
Shi Jiahai Department of Biological Sciences, National University of Singapore
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