[phenixbb] RuntimeError: Not enough memory for cubicles:

[Nathaniel Echols]

The ordered_solvent option is probably okay, but the peak/hole search  
is turned off by default in the current release (1.4-3).  Try  
upgrading and see if that fixes the problem.

thanks,
Nat

On Feb 26, 2009, at 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)
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb

-------------------
Nathaniel Echols
Lawrence Berkeley Lab
510-486-5136
NEchols at lbl.gov