[phenixbb] Death by Big-ass structure

[Paul Adams]

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
>
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> phenixbb at phenix-online.org
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-- 
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
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BLDG 64R0121
Berkeley, CA 94720, USA.
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