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RuntimeError: Not enough memory for cubicles:
by Gino Cingolani 26 Feb '09

26 Feb '09

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(a)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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Failed to carry out AutoBuild_parallel_omit
by Jhon Thomas 26 Feb '09

26 Feb '09

Hello all There is a problem with running phenix.autobuild. Failed to carry out AutoBuild_parallel_omit: child process stderr output: command: 'csh /home/thomas/phenix_omitmap/AutoBuild_run_1_/TEMP0/RUN_FILE_1' Badly placed ()'s. What could be solution. Thanks Thomas

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resolve.phenix and helices_strands_only
by Mo Wong 25 Feb '09

25 Feb '09

Hi all, I'm sure I've done this before, but could some please let me know/remind me what the correct syntax is for including "helices_strands_only=True" in a resolve script like the one below? phenix.resolve<<EOD hklin solve.mtz labin FP=FP SIGFP=SIGFP PHIB=PHIB FOM=FOM HLA=HLA HLB=HLB HLC=HLC HLD=HLD solvent_content 0.43 database 5 EOD Thanks!

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Select atoms by B-factors?
by Oliver Clarke 24 Feb '09

24 Feb '09

Hi, I'm currently refining a structure at 1.6A. Substantial portions of the structure are very well ordered, with B-factors < 15. I'd like to refine these well ordered regions using anisotropic thermal parameters, while keeping everything else isotropic. However, in doing so, the atom selections tend to become quite convoluted. Is there any way to select all atoms which initially have an isotropic B less than a certain cuttoff value? That way one could (after isotropic B-factor refinement) select the most ordered regions of the structure for anisotropic refinement. Cheers, Oliver Clarke

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links and REMARK 3 record in the final PDB
by Pascal Egea 23 Feb '09

23 Feb '09

Dear All, I apologize if this question has already been answered. I am refining a structure of a glycosylated-enzyme and I understood the way to define all the links (N-glycosylation to the ASN and beta-glycosidic bonds between the NAG units) and refinement is complete and everything is good. All the links I included in my cif_link definition file where taken into account and dealt with by Phenix (the .def and .geo files are fine). Is it normal however that in the resulting refined PDB file, no such links are written by PHENIX under the REMARK 3 record ? Same thing for the 5 disulfide bonds present in the protein. Thanks in advance for the clarification. Pascal Egea University of California San Francisco Department of Biochemistry and Biophysics Laboratory of Robert Stroud

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Please help with neutron composite SA-omit
by Anna Gardberg 23 Feb '09

23 Feb '09

Hello. I am attempting to create an SA-omit composite map with neutron scatterers. Unfortunately, phenix.autobuild data= "neutron.mtz" model="neutron_004.pdb" composite_omit_type=sa_omit scattering_table=neutron results in an error: "Sorry, unknown file or keyword: scattering_table=neutron Possibilities... (use 'phenix.autobuild --help all' to get full help): general.resolve_pattern_command_list=neutron density_modification.use_resolve_pattern=neutron decision_making.semi_acceptable_r=neutron decision_making.acceptable_r=neutron multiple_models.multiple_models_starting_resolution=neutron " Can someone here help, please? (For what it's worth: I'd use nCNS, but while CNS 1.21 (precompiled binaries) works on my computer, CNS 1.1 version seems to compile, it will not run. When I apply the nCNS patch to CNS 1.1, again it seems to compile, but will not run. ) Regards, Anna Gardberg

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Re: [phenixbb] Please help with neutron composite SA-omit
by Thomas C. Terwilliger 23 Feb '09

23 Feb '09

Hi again Anna, Can you possibly try this syntax for the "refine.eff" file: refinement{ main {scattering_table=neutron} } and then say phenix.autobuild <your usual parameters> refine_eff_file=refine.eff That should do it! All the best, -Tom T > Hello. > > I am attempting to create an SA-omit composite map with neutron > scatterers. > > Unfortunately, > > phenix.autobuild data= "neutron.mtz" model="neutron_004.pdb" > composite_omit_type=sa_omit scattering_table=neutron > > results in an error: > > "Sorry, unknown file or keyword: scattering_table=neutron > Possibilities... (use 'phenix.autobuild --help all' to get full help): > general.resolve_pattern_command_list=neutron > density_modification.use_resolve_pattern=neutron > decision_making.semi_acceptable_r=neutron > decision_making.acceptable_r=neutron > multiple_models.multiple_models_starting_resolution=neutron > " > > Can someone here help, please? > > (For what it's worth: I'd use nCNS, but while CNS 1.21 (precompiled binaries) works on my computer, CNS 1.1 version seems to compile, it will not run. When I apply the nCNS patch to CNS 1.1, again it seems to compile, but will not run. ) > > Regards, > Anna Gardberg > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb >

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Re: [phenixbb] Please help with neutron composite SA-omit
by Thomas C. Terwilliger 23 Feb '09

23 Feb '09

Hi Anna, Try putting your cmmand "scattering_table=neutron" in a "refine.eff" file and then run phenix.autobuild including the keyword refine_eff_file=refine.eff (note that you may need to specify the scope of scattering_table just as if you were using the command directly for phenix.refine) That is the way you can put any phenix.refine parameters into autobuild. Let me know if that doesn't do it! -Tom T > Hello. > > I am attempting to create an SA-omit composite map with neutron > scatterers. > > Unfortunately, > > phenix.autobuild data= "neutron.mtz" model="neutron_004.pdb" > composite_omit_type=sa_omit scattering_table=neutron > > results in an error: > > "Sorry, unknown file or keyword: scattering_table=neutron > Possibilities... (use 'phenix.autobuild --help all' to get full help): > general.resolve_pattern_command_list=neutron > density_modification.use_resolve_pattern=neutron > decision_making.semi_acceptable_r=neutron > decision_making.acceptable_r=neutron > multiple_models.multiple_models_starting_resolution=neutron > " > > Can someone here help, please? > > (For what it's worth: I'd use nCNS, but while CNS 1.21 (precompiled > binaries) works on my computer, CNS 1.1 version seems to compile, it > will not run. When I apply the nCNS patch to CNS 1.1, again it seems > to compile, but will not run. ) > > Regards, > Anna Gardberg > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb >

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DTT at special position
by Nikos Pinotsis 23 Feb '09

23 Feb '09

Dear all, even though I checked the documentation and previous threads I didn't find something relative to my problem: I have an elongated e-density that looks like DTT and appears to be located on a special position (there is actually an axis betwenn C2 and C3 atoms of DTT). Refining with phenix.refine using either 0.5 or 1.0 occupancy, I am getting the DTT molecule outside the density (and the symmetry related DTT from the other side and still in the middle the strong difference density. thanks in advance for any suggestions-solutions Nikos -- --------------------------------- Dr. Nikos Pinotsis Section of Structural Biology Institute of Cancer Research Chester Beatty Laboratories 237 Fulham Road London SW3 6JB, UK Tel: +44 20 7153 5453 / 5447 --------------------------------- The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.

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ADP refinement
by Katya Heldwein 20 Feb '09

20 Feb '09

Hi, I would like to use TLS refinement for protein (I have selected TLS groups) and individual isotropic refinement for water. How can I specify this in phenix.refine? Thanks, Katya -- Ekaterina Heldwein, Ph.D. Assistant Professor Department of Molecular Biology and Microbiology Tufts University School of Medicine 136 Harrison Ave Boston, MA 02111 phone: 617-636-0858 fax: 617-636-0337 e-mail: katya.heldwein(a)tufts.edu

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