Hi Frank, you should probably download the version 1.3 prerelease of PHENIX from the web page: http://www.phenix-online.org/download/index.html This may help. Cheers, Paul On May 25, 2007, at 8:12 AM, Frank von Delft wrote:
Hi, we get the memory error below for a structure of 30603 atoms 273217 reflections 2.1A H3 193.868 193.868 352.223 90.00 90.00 120.00 10x NCS
Anything I said? It's not THAT large a problem, I'd have thought, or should we go to the rhombohedral setting instead?
(Hmmmm, this rings a bell, wasn't there a posting about this 3 days ago? Nothing in the archives, was it CCP4bb?)
Cheers phx
Traceback (most recent call last): File "/usr/local/phenix/phenix-1.26b/phenix/phenix/command_line/ refine.py", line 5, in ? command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix/phenix-1.26b/phenix/phenix/refinement/ command_line.py", line 75, in run refine_object.run( File "/usr/local/phenix/phenix-1.26b/phenix/phenix/refinement/ driver.py", line 1236, in run log = log) File "/usr/local/phenix/phenix-1.26b/phenix/phenix/refinement/ strategies.py", line 273, in refinement_machine log = log) File "/usr/local/phenix/phenix-1.26b/phenix/phenix/refinement/ weight_xray_chem.py ", line 111, in __init__ self.fmodel_copy = self.fmodel.deep_copy() File "/usr/local/phenix/phenix-1.26b/mmtbx/mmtbx/twinning/ twin_f_model.py", line 1003, in deep_copy map_types = self.map_types File "/usr/local/phenix/phenix-1.26b/mmtbx/mmtbx/twinning/ twin_f_model.py", line 888, in __init__ self.update_f_mask() File "/usr/local/phenix/phenix-1.26b/mmtbx/mmtbx/twinning/ twin_f_model.py", line 1370, in update_f_mask self.f_mask_array = mask.structure_factors( self.miller_set ) File "/usr/local/phenix/phenix-1.26b/mmtbx/mmtbx/masks.py", line 103, in structure_factors flex.grid(fft_manager.m_real()).set_focus(fft_manager.n_real())) MemoryError
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
-- Paul Adams Senior Staff Scientist, Physical Biosciences Division Head, Berkeley Center for Structural Biology Deputy Principal Investigator, Berkeley Structural Genomics Center Building 64, Room 248 Tel: 510-486-4225, Fax: 510-486-5909 http://cci.lbl.gov/ Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. --