[phenixbb] Death by Big-ass structure

Frank von Delft frank.vondelft at sgc.ox.ac.uk
Fri May 25 08:12:54 PDT 2007


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




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