[phenixbb] Death by Big-ass structure

[Peter Zwart]

Sorry, not wearing  glasses at the moment.
Okai. reindexing should work like Ulrich said.

I'll send a script that should take care of business in a minute.

Peter




2007/5/25, Frank von Delft <frank.vondelft at sgc.ox.ac.uk>:
> 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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