[phenixbb] RunTime_errors

Xue-Yuan Pei xyp20 at mole.bio.cam.ac.uk
Thu Jan 21 04:29:13 PST 2010

Dear phenix experts:
I have a data in R32 at 2.3A. 4 molecules/A.U. I got the following 
error message when I run refinement wiht phenix v1.5-2:

=============================== refinement start 

Traceback (most recent call last):
   File "/usr/local/phenix-1.5-2/phenix/phenix/command_line/refine.py", 
line 11, in <module>
     command_line.run(command_name="phenix.refine", args=sys.argv[1:])
   File "/usr/local/phenix-1.5-2/phenix/phenix/refinement/command_line.py", 
line 89, in run
   File "/usr/local/phenix-1.5-2/phenix/phenix/refinement/driver.py", line 
1121, in run
     call_back_handler       = call_back_handler)
   File "/usr/local/phenix-1.5-2/phenix/phenix/refinement/strategies.py", 
line 185, in refinement_machine
     log                           = log)
   File "/usr/local/phenix-1.5-2/cctbx_project/mmtbx/utils.py", line 1371, 
in fmodel_manager
     max_number_of_bins           = max_number_of_resolution_bins)
   File "/usr/local/phenix-1.5-2/cctbx_project/mmtbx/f_model.py", line 358, 
in __init__
     mask_params       = self.mask_params)
   File "/usr/local/phenix-1.5-2/cctbx_project/mmtbx/masks.py", line 175, 
in __init__
     self.compute_f_mask(twin = twin)
   File "/usr/local/phenix-1.5-2/cctbx_project/mmtbx/masks.py", line 264, 
in compute_f_mask
     asu_mask.compute(sites_frac, atom_radii)
RuntimeError: mmtbx Error: the mask grid size: 576 * 576 * 270 = 89579520 
is too big
  maximum allowed size is 67108863 64 bit OS and software might be required 
for such a big mask.

How can I tackle this problem? Any suggestion is highly appreciated.


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