Hi Gino, sorry for the problem. Please use the latest version of PHENIX: http://www.phenix-online.org/download/ As already suggested, try setting (this is the default in the latest version): show_residual_map_peaks_and_holes=False this most likely will help. If not, to further reduce the memory consumption try using these parameters all at once: refinement { output { write_maps = False } electron_density_maps { grid_resolution_factor = 1/3. } main { show_residual_map_peaks_and_holes = False } ordered_solvent { correct_drifted_waters = False } peak_search { resolution_factor = 1./3. } mask { grid_step_factor = 3.0 } } The word "cubicles" tells me that this is not a memory problem though... Anyway, setting "show_residual_map_peaks_and_holes=False" or using the latest version should help. But it will actually hide the problem. If you want us to debug it and so prevent it in future, we will need to have the data, model and the exact command you used. Pavel. 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: [email protected] *********************************************************** "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 [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb