[phenixbb] RuntimeError: Not enough memory for cubicles:

[Pavel Afonine]

Yes, this is a good idea!
Pavel.


On 2/26/09 6:23 PM, Nigel W Moriarty wrote:
> 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)
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://www.phenix-online.org/mailman/listinfo/phenixbb
>>
>>   
>>     
>
>   
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20090226/4c32e158/attachment-0003.htm>