[phenixbb] fix rotamers
Pavel Afonine
PAfonine at lbl.gov
Fri Apr 9 07:48:31 PDT 2010
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
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