[phenixbb] fix rotamers

Robert Ng ng.ng.robert at gmail.com
Fri Apr 9 07:15:43 PDT 2010

Dear all,

I want to do fix rotamers with the phenix with my 3A resolution virus
data. Just do some try out.
But I got the memory error listed below:
Traceback (most recent call last):
  File "/usr/local/phenix-1.6.1-348/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-1.6.1-348/phenix/phenix/refinement/command_line.py",
line 89, in run
  File "/usr/local/phenix-1.6.1-348/phenix/phenix/refinement/driver.py",
line 1170, in run
    call_back_handler       = call_back_handler)
  File "/usr/local/phenix-1.6.1-348/phenix/phenix/refinement/strategies.py",
line 570, in refinement_machine
    params                      = params.fit_side_chains)
  File "/usr/local/phenix-1.6.1-348/cctbx_project/mmtbx/refinement/fit_rotamers.py",
line 779, in run
    map_sel = flex.abs(residual_map_data) < params.filter_residual_map_value

Does anybody has this problem before ? and know how to fix this ?


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