Greetings fellow crystallographers,<br><br>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:<br>
<br>Traceback (most recent call last):<br>� File "/programs/phenix-1.5-2/phenix/phenix/command_line/refine.py", line 11, in <module><br>��� command_line.run(command_name="phenix.refine", args=sys.argv[1:])<br>
� File "/programs/phenix-1.5-2/phenix/phenix/refinement/command_line.py", line 89, in run<br>��� call_back_handler=call_back_handler)<br>� File "/programs/phenix-1.5-2/phenix/phenix/refinement/driver.py", line 1121, in run<br>
��� call_back_handler������ = call_back_handler)<br>� File "/programs/phenix-1.5-2/phenix/phenix/refinement/strategies.py", line 428, in refinement_machine<br>��� monitors�� = monitors)<br>� File "/programs/phenix-1.5-2/cctbx_project/mmtbx/refinement/rigid_body.py", line 559, in __init__<br>
��� out��� = log)<br>� File "/programs/phenix-1.5-2/cctbx_project/mmtbx/refinement/rigid_body.py", line 619, in show<br>��� translations=t_vec)<br>� File "/programs/phenix-1.5-2/cctbx_project/mmtbx/refinement/print_statistics.py", line 161, in show_rigid_body_rotations_and_translations<br>
��� % euler_angle_convention, suffix=frame)<br>� File "/programs/phenix-1.5-2/cctbx_project/libtbx/utils.py", line 652, in write<br>��� file_object.write(str)<br>IOError: [Errno 5] Input/output error<br><br>Again, the only thing I've done is made a few rigid body and tls groups. Please advise!<br>
<br>Thanks,<br>Geoff<br clear="all"><br>-- <br>Geoffrey K. Feld<br><br>Department of Chemistry<br>492 Stanley Hall<br>University of California, Berkeley<br><br>"Vigilia pretium libertatis"<br>