[phenixbb] input/output error

Geoffrey Feld gkfeld at berkeley.edu
Mon Dec 14 11:31:13 PST 2009

Greetings fellow crystallographers,

This past weekend, I collected some new data on my new project, indexed,
scaled it, and found a phaser solution. The resolution is 3.6 A and I need
to find one of the protein components, so I'm slowly refining piece-by-piece
so I don't overdo it and flatten out the missing protein. To do this, I
simply do rigid body and tls refinements for decreasingly smaller pieces of
the protein I've already found. This method worked for me in the past for a
similar structure. However, this time, as the refinement is finishing up, I
get an input/output error and the program shuts down. Sometimes I get
similar errors, and I can fix them by simply running the job again,
overwriting the failed job, but this time that doesn't seem to be working.
Here's the output from my .log file:

Traceback (most recent call last):
  File "/programs/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 "/programs/phenix-1.5-2/phenix/phenix/refinement/command_line.py",
line 89, in run
  File "/programs/phenix-1.5-2/phenix/phenix/refinement/driver.py", line
1121, in run
    call_back_handler       = call_back_handler)
  File "/programs/phenix-1.5-2/phenix/phenix/refinement/strategies.py", line
428, in refinement_machine
    monitors   = monitors)
"/programs/phenix-1.5-2/cctbx_project/mmtbx/refinement/rigid_body.py", line
559, in __init__
    out    = log)
"/programs/phenix-1.5-2/cctbx_project/mmtbx/refinement/rigid_body.py", line
619, in show
line 161, in show_rigid_body_rotations_and_translations
    % euler_angle_convention, suffix=frame)
  File "/programs/phenix-1.5-2/cctbx_project/libtbx/utils.py", line 652, in
IOError: [Errno 5] Input/output error

Again, the only thing I've done is made a few rigid body and tls groups.
Please advise!


Geoffrey K. Feld

Department of Chemistry
492 Stanley Hall
University of California, Berkeley

"Vigilia pretium libertatis"
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