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Lost my job history, can it be recovered? (GUI)
by Andrew Waight 02 Aug '12

02 Aug '12

Hello All, It just so happened that my lab's server ran out of space (someone else uploading datasets) while my phenix rosetta MR job was running. Now the GUI no longer shows any job history in the job history tab (although on the title page the number of jobs is correctly displayed. I cannot find any information on how or if its possible to recover my job history in the GUI. Any tips? Thanks so much. Drew

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July 2012 Computational Crystallography Newsletter
by Nigel Moriarty 31 Jul '12

31 Jul '12

Folks The latest issue of the Computational Crystallography Newsletter is available on-line at http://www.phenix-online.org/newsletter for download. The articles are of general interest to protein crystallographers and are listed below. Enjoy Nigel Moriarty Articles ----------- cctbx tools for transparent job execution on clusters On the analysis of residual density distributions on an absolute scale Short communications -------------------------------- DETAC: tools to detect alternative conformations by unrestrained refinement ERRASER, a powerful new system for correcting RNA models Fitting tips - Rotamer correction with backrub -- Nigel W. Moriarty, PhD Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov

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what installer would work with a cluster with Darwin 9.8.0 if any?
by Tatyana Sysoeva 27 Jul '12

27 Jul '12

Hi all, I am starting to use a new computer cluster and just found out by uname that it runs Darwin OS? It is totally new to me and I am wondering if Phenix would run on it? should I use just some Mac installer? I would really appreciate any advices! Thank you! Sincerely, Tanya

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Re: [phenixbb] what installer would work with a cluster with Darwin 9.8.0 if any?
by Tatyana Sysoeva 27 Jul '12

27 Jul '12

Thank you Miguel and Ben! I did found the newest release at the cluster after I learned how to use "find" properly! In particular, thank you for pointing out the script to source! Best regards, Tanya

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refinement problem
by Afshan Begum 27 Jul '12

27 Jul '12

Dear Experts I am refining my structures in windows mode and every time i got this crash message i do not know how to solve this issue? If any one encountered this problem kindly suggest me how to solve it. While when i refine with refmac the file proceeds smoothly but i want to refinement in phenix due to utilize some parameters. its end like this: Exporting results ============================== Writing refined structure to PDB file: C:\Documents and Settings\pc user\Desktop\Refine_2\jbu_refine_2.pdb n_use = 7514 n_use_u_both = 7514 n_use_u_iso = 0 n_use_u_aniso = 0 n_grad_site = 0 n_grad_u_iso = 0 n_grad_u_aniso = 0 n_grad_occupancy = 331 n_grad_fp = 0 n_grad_fdp = 0 total number of scatterers = 7514 After that its not produce the map file and gave errore crash mesage. <module> Bus error (Python call stack above) This crash may be due to a problem in any imported Python module, including modules which are not part of the cctbx project. To disable the traps leading to this message, define these environment variables (e.g. assign the value 1): BOOST_ADAPTBX_FPE_DEFAULT BOOST_ADAPTBX_SIGNALS_DEFAULT This will NOT solve the problem, just mask it, but may allow you to proceed in case it is not critical. Your suggestion highly obliged I would be very thankful to you AFSHAN

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need help
by Afshan Begum 25 Jul '12

25 Jul '12

Dear Experts I am refining my structures in windows mode and every time i got this crash message i do not know how to solve this issue? If any one encountered this problem kindly suggest me how to solve it. While when i refine with refmac the file proceeds smoothly but i want to final refinement in phenix due to utilize some parameters.its end like this: Exporting results ============================== Writing refined structure to PDB file: C:\Documents and Settings\pc user\Desktop\Refine_2\jbu_refine_2.pdb n_use = 7514 n_use_u_both = 7514 n_use_u_iso = 0 n_use_u_aniso = 0 n_grad_site = 0 n_grad_u_iso = 0 n_grad_u_aniso = 0 n_grad_occupancy = 331 n_grad_fp = 0 n_grad_fdp = 0 total number of scatterers = 7514 After that its not produce the map file and gave errore crash mesage file attached. Your suggestion highly obliged I would be very thankful to you Best Regards AFSHAN

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problem on phenix refine 2
by herohonan 21 Jul '12

21 Jul '12

Hi all: I do not know if someone mentioned this problem here before. Recently I ran the AutoBuild to build the structure model, and it outputs a best model(R/Rfree 0.20/0.24). After that, I tried the program Phenix Refine using the .pdb and .mtz generated by AutoBuild. The R value increased to 0.23/0.30 by the end of this refine. I wonder why this happened? Or if I have done something wrong? (After AutoBuild, I modified the structure and added the substrate moleculars into the structure by hand. I thought the increase of the R value was resulted from the inapposite position of the substrates. But the R value still increased when I ran the Phenix Refine just by inputting the output of the AutoBuild without any manual modification.) -- Tong Huo Ph.D candidate College of Life Sciences Nankai University Tianjin, China

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problem on phenix refine
by 霍彤 20 Jul '12

20 Jul '12

Hi all: I do not know if someone mentioned this problem here before. Recently I ran the AutoBuild to build the structure model, and it outputs a best model(R/Rfree 0.20/0.24). After that, I tried the program Phenix Refine using the .pdb and .mtz generated by AutoBuild. The R value increased to 0.23/0.30 by the end of this refine. I wonder why this happened? Or if I have done something wrong? --

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problems with eLBOW: RuntimeError: Bond distance > max_reasonable_bond_distance: 696.942 > 500:
by Gino Cingolani 19 Jul '12

19 Jul '12

Hi all (Nigel), I'm trying the generate restraints for a large structure that also contains 12 ANPs, 4 ADPa and a a few more ions. When i run "phenix.elbow --do-all MR.1.pdb", phenix crashes with the following... ------------------------------------------------------------------------------ electronic Ligand Builder & Optimisation Workbench (eLBOW) 1.8 1069 - Nigel W. Moriarty (NWMoriarty(a)LBL.Gov) ------------------------------------------------------------------------------ Input format is PDB MoleculeClass : C:20 N:11 O:22 P: 5 (PDB format) 58 atoms 0 bonds 0 angles 0 dihedrals 0 rings Molecule was trimmed MoleculeClass : C:10 N: 6 O:12 P: 3 (PDB format) 31 atoms 0 bonds 0 angles 0 dihedrals 0 rings Predicted memory usage by semi-empirical method : 47Mb Timing estimates Python portion / ATP : 100% c++ optimisation cycle / ATP : 100% Hydrogens may be required to determine the correct bonding 0:05 Hydrogenise Hydrogenise Hydrogenise Hydrogenise Hydrogenise Hydrogenise H Traceback (most recent call last): File "/usr/local/phenix-1.8-1069/build/intel-linux-2.6-x86_64/../../elbow/elbow/command_line/builder.py", line 2240, in <module> run() File "/usr/local/phenix-1.8-1069/build/intel-linux-2.6-x86_64/../../elbow/elbow/command_line/builder.py", line 2038, in run molecule = builder(molecule, options) File "/usr/local/phenix-1.8-1069/build/intel-linux-2.6-x86_64/../../elbow/elbow/command_line/builder.py", line 870, in builder pre_optimise_selections=pre_optimise_selections, File "/usr/local/phenix-1.8-1069/elbow/elbow/utilities/OptimiseMixins.py", line 1009, in ExplodeAndOptimise opt_cycles=1, File "/usr/local/phenix-1.8-1069/elbow/elbow/utilities/OptimiseMixins.py", line 270, in OptimiseSelectedAtoms show_geo=show_geo, File "/usr/local/phenix-1.8-1069/elbow/elbow/utilities/OptimiseMixins.py", line 673, in OptimiseCCTBXProgression additional_restraints=additional_restraints, File "/usr/local/phenix-1.8-1069/elbow/elbow/cctbx_api/CCTBXMixins.py", line 262, in GetNewManager debug=debug, File "/usr/local/phenix-1.8-1069/elbow/elbow/cctbx_api/geometry_manager.py", line 173, in run pair_proxies = manager.pair_proxies(sites_cart=sites_cart) File "/usr/local/phenix-1.8-1069/cctbx_project/cctbx/geometry_restraints/manager.py", line 595, in pair_proxies check_bonded_distance_cutoff(sites_cart=sites_cart) File "/usr/local/phenix-1.8-1069/cctbx_project/cctbx/geometry_restraints/manager.py", line 499, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 696.942 > 500: distance: 1 - 31: 478.879 distance: 2 - 32: 603.994 distance: 5 - 33: 595.912 distance: 7 - 34: 479.110 distance: 13 - 35: 389.539 distance: 13 - 36: 559.710 distance: 14 - 37: 561.219 distance: 16 - 38: 696.942 distance: 17 - 39: 571.138 distance: 18 - 40: 497.529 distance: 19 - 41: 593.584 distance: 20 - 42: 483.447 distance: 22 - 43: 566.195 distance: 26 - 44: 561.483 distance: 26 - 45: 470.865 distance: 28 - 46: 628.947 Any clues? All nucleotides look good by eye. Thanks, Gino ****************************************************************************** Gino Cingolani, Ph.D. Associate Professor Thomas Jefferson University Dept. of Biochemistry & Molecular Biology 233 South 10th Street - Room 826 Philadelphia PA 19107 Office (215) 503 4573 Lab (215) 503 4595 Fax (215) 923 2117 E-mail: gino.cingolani(a)jefferson.edu Website: http://www.cingolanilab.org ****************************************************************************** "Nati non foste per viver come bruti, ma per seguir virtute e canoscenza" ("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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Collect MR solution to same ASU?
by Francis E Reyes 17 Jul '12

17 Jul '12

I remember there being a phenix cmd line utility that collects MR solutions to the same asymmetric unit. Or was I dreaming? F --------------------------------------------- Francis E. Reyes PhD 215 UCB University of Colorado at Boulder

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