[phenixbb] Death by Big-ass structure
Ulrich Baumann
ulrich.baumann at ibc.unibe.ch
Fri May 25 08:44:54 PDT 2007
Hi Frank,
I had the same problem. Rhombohedral setting helped. Unfortunately the
reindex.py does not reindex FreeR flags :-(
Best wishes,
Uli
On Fri, 25 May 2007 17:12:54 +0200, Frank von Delft
<frank.vondelft at sgc.ox.ac.uk> 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
>
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--
Prof Ulrich Baumann
Departement für Chemie und Biochemie
Freiestrasse 3
Ch-3012 Bern, Switzerland
phone + 41 (0)31 631 4320/4343
fax + 41 (0) 31 631 4887
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