[phenixbb] memory error

Anastasia A Aksyuk aaksyuk at bio.purdue.edu
Mon Sep 22 08:53:15 PDT 2008


Hello everyone!
I  have the following error when using phenix-1.3-final:

/========================== Target weights: x-ray data 
=========================

Traceback (most recent call last):
  File 
"/usr/local/rossmann/phenix/phenix-1.3-final/phenix/phenix/command_line/refine.py", 
line 5, in <module>
    command_line.run(command_name="phenix.refine", args=sys.argv[1:])
  File 
"/usr/local/rossmann.master/phenix/phenix-1.3-final/phenix/phenix/refinement/command_line.py", 
line 89, in run
  File 
"/usr/local/rossmann.master/phenix/phenix-1.3-final/phenix/phenix/refinement/driver.py", 
line 1081, in run
  File 
"/usr/local/rossmann.master/phenix/phenix-1.3-final/phenix/phenix/refinement/strategies.py", 
line 472, in refinement_machine
  File 
"/usr/local/rossmann.master/phenix/phenix-1.3-final/phenix/phenix/refinement/weight_xray_chem.py", 
line 264, in __init__
  File 
"/usr/local/rossmann.master/phenix/phenix-1.3-final/phenix/phenix/refinement/weight_xray_chem.py", 
line 307, in xyz_weights
  File 
"/usr/local/rossmann.master/phenix/phenix-1.3-final/phenix/phenix/refinement/weight_xray_chem.py", 
line 196, in __init__
  File 
"/usr/local/rossmann/phenix/phenix-1.3-final/mmtbx/mmtbx/__init__.py", 
line 72, in update_xray_structure
    force_update_f_mask = force_update_f_mask)
  File 
"/usr/local/rossmann/phenix/phenix-1.3-final/mmtbx/mmtbx/f_model.py", 
line 675, in update_xray_structure
    force_update       = force_update_f_mask)
  File 
"/usr/local/rossmann/phenix/phenix-1.3-final/mmtbx/mmtbx/masks.py", line 
207, in f_mask
    return self.compute_f_mask()
  File 
"/usr/local/rossmann/phenix/phenix-1.3-final/mmtbx/mmtbx/masks.py", line 
222, in compute_f_mask
    miller_set = self.miller_array)
  File 
"/usr/local/rossmann/phenix/phenix-1.3-final/mmtbx/mmtbx/masks.py", line 
138, in structure_factors
    flex.grid(fft_manager.m_real()).set_focus(fft_manager.n_real()))
MemoryError 

/I am running with defaults, i.e. the following command:
phenix.refine se.water2.noano_001-2acetate-noH-coot-0.pdb 
cr2remote.cr3.1.8-2_scaleit1.mtz ray_data.r_free_flags.test_flag_value=1 
output.prefix=se.noano2.acetate 
refinement.input.xray_data.labels="F_peak(+),SIGF_peak(+),F_peak(-),SIGF_peak(-),merged"

I would greatly appreciate your help to resolve this issue and I can 
provide any additional information needed.
Thank you,
Anastasia




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