Hi Robert, the error message tells me that phenix.refine needed more memory than available on your computer. In general, fix_rotamers is a memory demanding option since at some point phenix.refine computes 3 maps at once: 2mFo-DFc, mFo-DFc, and Fc maps. If you have an access to a machine with more memory you can run this command phenix.refine model.pdb data.mtz fix_rotamers=true --show-process-info to see how much memory this run needed (the job needs to finish, and look towards the end of .log file for the last memory footprint). Alternatively, you can send me data and model and I will run the above command for you. Pavel. On 4/9/10 7:15 AM, Robert Ng wrote:
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 call_back_handler=call_back_handler) 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 MemoryError
Does anybody has this problem before ? and know how to fix this ?
Robert _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb