February 2007 - phenixbb - phenix-online.org

phenix.refine crash
by Jianghai Zhu 19 Mar '07

19 Mar '07

Hi, I was using phenix.refine from the latest cci apps bundle to do tls +individual_sites+individual_adp refinement. The program crashed with the following error message. ----------Target weights (before refinement)---------- Traceback (most recent call last): File "/nfs/home/jzhu/cci_apps_sources/phenix/phenix/command_line/ refine.py", line 5, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/nfs/home/jzhu/cci_apps_sources/phenix/phenix/refinement/ command_line.py", line 75, in run call_back_after_monitor_collect=call_back_after_monitor_collect) File "/nfs/home/jzhu/cci_apps_sources/phenix/phenix/refinement/ driver.py", line 1108, in run log = log) File "/nfs/home/jzhu/cci_apps_sources/phenix/phenix/refinement/ strategies.py", line 245, in refinement_machine log = log) File "/nfs/home/jzhu/cci_apps_sources/phenix/phenix/refinement/ weight_xray_chem.py", line 222, in __init__ compute_gradients = True) File "/nfs/home/jzhu/cci_apps_sources/mmtbx/mmtbx/restraints.py", line 144, in energies_adp_aniso xray_structure = xray_structure, File "/nfs/home/jzhu/cci_apps_sources/cctbx/cctbx/adp_restraints/ __init__.py", line 109, in __init__ self.check_flags(fl_i) File "/nfs/home/jzhu/cci_apps_sources/cctbx/cctbx/adp_restraints/ __init__.py", line 177, in check_flags assert not fl.use_u_aniso() AssertionError Anyone has any idea what is happening? Thanks. Jianghai +++++++++++++++++++++++++++++++ Jianghai Zhu, Ph.D CBR Institute for Biomedical Research Department of Pathology Harvard Medical School 200 Longwood Ave., Boston, MA 02115 Ph: 617-278-3211 Fx: 618-278-3232 +++++++++++++++++++++++++++++++

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Phased anomalous difference map
by Luca Jovine 28 Feb '07

28 Feb '07

Hello, Is it possible to calculate a phased anomalous difference map with phenix.refine? Thanks, Luca

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Re: [phenixbb] phenix.refine crash
by Ralf W. Grosse-Kunstleve 25 Feb '07

25 Feb '07

> Anyone has any idea what is happening? Thanks. It is a bug that we've fixed already. We will release a new cci apps in the next couple of days that will include the fix. In the meantime, could you try removing the ANISOU cards (grep -v ANISOU xxx.pdb)? I think that should work around the problem. Ralf

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Re: [phenixbb] input HA
by Tom Terwilliger 13 Feb '07

13 Feb '07

Hi Morton, I'm sorry to make it difficult! Here are 2 formats that should work: 1. PDB format (I'm not sure why the one from cns failed...can you send me a line or two from that so I can make it work?): HETATM 1 SE SE 3 73.920 0.324 3.857 0.92 54.60 Se HETATM 2 SE SE 4 39.591 8.262 2.158 0.55 60.00 Se 2. Plain fractional xyz, with or without the word "xyz". For example see: $PHENIX/examples/gene-5-mad/sites.xyz : xyz 0.0271 0.8074 0.0657 xyz 0.0239 0.0116 -0.0965 Please let me know if this doesn't do it! -Tom T At 03:52 AM 2/13/2007, Morten Grøftehauge wrote: >Ok, I give up. > >What is the correct format for a heavy atom file >for AutoSOL? I've tried both the outputs from >FFT, CNS pdbs and sdbs and I've tried just >putting them on a line like you do for SHARP: >ATOM Br - 0.0120 0.5731 0.2740 >but none of them are accepted by Phenix. >Any help please? > >-- >Morten K Grøftehauge >PhD student >Department of Molecular Biology >Gustav Wieds Vej 10 C >8000 Aarhus C - Denmark >Phone: +45 89 42 50 10 >Fax: +45 86 12 31 78 ><http://www.bioxray.dk>www.bioxray.dk > >_______________________________________________ >phenixbb mailing list >phenixbb(a)phenix-online.org >http://www.phenix-online.org/mailman/listinfo/phenixbb Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: terwilliger(a)LANL.gov Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB

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input HA
by Morten Grøftehauge 13 Feb '07

13 Feb '07

Ok, I give up. What is the correct format for a heavy atom file for AutoSOL? I've tried both the outputs from FFT, CNS pdbs and sdbs and I've tried just putting them on a line like you do for SHARP: ATOM Br -0.0120 0.5731 0.2740 but none of them are accepted by Phenix. Any help please? -- Morten K Grøftehauge PhD student Department of Molecular Biology Gustav Wieds Vej 10 C 8000 Aarhus C - Denmark Phone: +45 89 42 50 10 Fax: +45 86 12 31 78 www.bioxray.dk

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