[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 

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.


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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