[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
More information about the phenixbb
mailing list