[phenixbb] RuntimeError: Not enough memory for cubicles:

Nigel W Moriarty NWMoriarty at lbl.gov
Thu Feb 26 18:23:36 PST 2009


Gino

You could also try

main.number_of_macro_cycles=0 

to test that the refinement will terminate safely.

Nigel

On 2/26/09 6:01 PM, Gino Cingolani wrote:
> Hi,
>
> I'm refining a huge structure with ~13,000 residues in the asymmetric unit.
> I started a massive job with the following inputs:
>
> phenix.refine data.mtz model.pdb
> ordered_solvent=true
> strategy=individual_sites+group_adp+tls 
> tls_group_selections.params 
> main.ncs=true
> main.number_of_macro_cycles=10 
>
> After >24 h the Rfree had dropped from 45% to 33%, but at the very end, 
> just before outputting the refined pdb model, Phenix died with the following
> error message:
>
>
> ############################################################
> Hello all========== residual map mFobs-DFmodel: highest peaks and deepst
> holes =========
>                            ----------peaks----------
>
> Traceback (most recent call last):
>   File "/usr/local/phenix-1.3-final/phenix/phenix/command_line/refine.py",
> line 5, in <module>
>     command_line.run(command_name="phenix.refine", args=sys.argv[1:])
>   File
> "/usr/local/phenix-1.3-final/phenix/phenix/refinement/command_line.py", line
> 89, in run
>     call_back_after_monitor_collect=call_back_after_monitor_collect)
>   File "/usr/local/phenix-1.3-final/phenix/phenix/refinement/driver.py",
> line 1081, in run
>     call_back_after_monitor_collect = call_back_after_monitor_collect)
>   File "/usr/local/phenix-1.3-final/phenix/phenix/refinement/strategies.py",
> line 724, in refinement_machine
>     fmodels=fmodels, model=model, log=log)
>   File "/usr/local/phenix-1.3-final/phenix/phenix/refinement/strategies.py",
> line 752, in highest_peaks_and_deepest_holes_in_residual_map
>     log = log)
>   File "/usr/local/phenix-1.3-final/mmtbx/mmtbx/find_peaks.py", line 210, in
> show_highest_peaks_and_deepest_holes
>     log        = log)
>   File "/usr/local/phenix-1.3-final/mmtbx/mmtbx/find_peaks.py", line 117, in
> __init__
>     map = fft_map_data).all(max_clusters = max_number_of_peaks)
>   File "/usr/local/phenix-1.3-final/cctbx/cctbx/maptbx/__init__.py", line
> 196, in peak_search
>     max_clusters=parameters.max_clusters())
>   File "/usr/local/phenix-1.3-final/cctbx/cctbx/maptbx/__init__.py", line
> 303, in __init__
>     general_positions_only=self._general_positions_only)
>   File "/usr/local/phenix-1.3-final/cctbx/cctbx/crystal/__init__.py", line
> 477, in site_cluster_analysis
>     cubicle_epsilon=cubicle_epsilon)
> RuntimeError: Not enough memory for cubicles:
>   This may be due to unreasonable parameters:
>     cubicle_edge=0.7
>     space_span=(293.298,92.903,214.527)
>     n_cubicles=(419,133,307)
>     max_number_of_bytes=1724676096
>
>
> ######################################################
>
> Any suggestion on what to do?
> As invididual refinement modules (e.g. regular rigid body refinemnet, SA,
> energy minimization, TLS, etc)
> run OK, is the problem coming from the  "ordered_solvent=true" command?
> Thanks in advance!
>
>
> Gino Cingolani, Ph.D.
>
> ***********************************************************
> Gino Cingolani, Ph.D.
> Assistant Professor
> Dept. of Biochemistry and Molecular Biology
> SUNY Upstate Medical University
> 750 E. Adams Street, Syracuse, NY, 13210
> Tel.   (315) 464 8744
> Fax.  (315) 464 8750
> Email:  cingolag at upstate.edu
> ***********************************************************
> "Nati non foste per viver come bruti,  ma per seguir virtute e conoscenza"
> ("You were not born to live like brutes, but to follow virtue and
> knowledge")
> Dante, The Divine Comedy (Inferno,  XXVI, vv. 119-120)
> _______________________________________________
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> phenixbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb
>
>   

-- 
Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709
Fax   : 510-486-5909
Email : NWMoriarty at LBL.gov
Web   : CCI.LBL.gov




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