- phenixbb - phenix-online.org

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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CCP4 6.3.0 released
by ronan.keegan＠stfc.ac.uk 16 Jul '12

16 Jul '12

Dear All, We're very pleased to announce the release of the latest version of the CCP4 Software Suite. Version 6.3.0 (Settle) is now available from the CCP4 download website: http://www.ccp4.ac.uk/download.php The release is available for Linux, Mac OSX and Windows platforms, and delivers a number of new programs, updates and features: 1. New Components and Updates: New: Aimless (Scaling and Merging, replacement for Scala) Prosmart (Generation of external restraints for Refmac) Nautilus (Automatic building of RNA/DNA) Ample (Automatic Ab initio modelling for Molecular Replacement) Dimple (Automatic difference map calculation) Zanuda (Space group checker/validator) CMapCut (Preparation of electron-density search model for MR) Comit (Composite omit maps) Gesamt (Structure aligner not using secondary structure assignments) ViewHKL (Graphical viewer for reflection data) Updated: Mosflm v7.0.9 (Data processing/reduction) iMosflm v1.0.7 (Mosflm GUI) Pointless v1.6 (Laue group determination) Refmac v5.7 (Macromolecular refinement) Phaser v2.5.1 (Molecular Replacement and Experimental Phasing) MrBump (Automatic Molecular Replacement, now includes phaser.sculptor models) Xia2 (Automated data reduction) CCP4mg v2.6.2 (CCP4 Molecular Graphics, much improved on features and stability) CCP4 Graphical User Interface: - new automation module - provides interfaces for new and updated modules - ViewHKL option for viewing reflection (mtz) files More information on updates is available from: http://www.ccp4.ac.uk/html/CHANGESinV6_3.html 2. ARP/wARP co-distribution Release 6.3.0 marks a milestone in collaboration between CCP4 and ARP/wARP teams by releasing ARP/wARP Model Building software v7.3 jointly with CCP4 Software Suite. In order to get ARP/wARP Software, academic users need only to select the appropriate package from download pages or with our new Package Manager, and type in their name and e-mail address where required. Commerical users will be required also to provide their reference number, obtainable separately from EMBL-EM. ARP/wARP 7.3 includes the following major updates and changes (on behalf of Victor Lamzin): - The protocols for the use of NCS in protein chain tracing have been improved and expanded to a wider range of resolutions. - Common ligands can now be automatically identified and fit into a specified electron density. - The algorithm for modelling partial ligands (cocktail screening) has been replaced with a new one that applies a number of sophisticated numerical features - The ARP/wARP graphics front-end, ArpNavigator, automatically assigns secondary structure and has an improved visual presentation of a static model or real time protein or ligand building. - Supported computer platforms are Mac powerpc, Mac Intel and Linux (including 32 and 64-bit versions). - The ARP/wARP installer has been considerably updated on all platforms. - Joint software release and authentication with the CCP4 is now possible. - CCP4 6.3.0 and Refmac 5.7.0029 are the recommended versions to use with ARP/wARP 7.3. 3. 64-bit precompiled packages Starting with version 6.3.0, CCP4 distributes both 32-bit and 64-bit precompiled binaries for Linux. Note that 64-bit codes will not run on 32-bit architectures, and 32-bit codes will run on 64-bit setups only if 32-bit libraries are installed (not a default for most Linuxes). THEREFORE: PLEASE MAKE SURE THAT YOU HAVE SET THE 32-bit/64-bit SWITCH ON TOP OF THE DOWNLOAD PAGES CORRECTLY BEFORE ALL! 4. "Friendly" Coot and CCP4mg distributions Coot is known to be less portable than the rest of CCP4 Program Suite. CCP4mg is more portable and requires special builds only for older Linuxes. Our new Package Manager will try to automatically choose Coot and CCP4mg bundles that are most appropriate for your system. In addition, our new download pages will offer you a range of precompiled Coot and CCP4mg packages, from where you may choose ones that work for you. 5. New distribution mechanism We hope that you will find our new Download Pages more intuitive and convenient than before. We have worked hard to improve our Windows installer, to make it working faster and smoother. On Linux and Mac platforms, we recommend using Package Manager, a small graphical application that allows you to select the desired components, and automatically download and install them on your system. Note that Package Manager features resumable downloads, which may be useful for users with slow or less reliable Internet connection. We would like to thank all of the developers who have contributed into CCP4 6.3.0, and all of those who have helped in testing it. The following publication should be used to cite the use of CCP4: M. D. Winn, C. C. Ballard, K. D. Cowtan, E. J. Dodson, P. Emsley, P. R. Evans, R. M. Keegan, E. B. Krissinel, A. G. W. Leslie, A. McCoy, S. J. McNicholas, G. N. Murshudov, N. S. Pannu, E. A. Potterton, H. R. Powell, R. J. Read, A. Vagin and K. S. Wilson (2011) Overview of the CCP4 suite and current developments, Acta Cryst D67 235-242. CCP4 is supported by the BBSRC UK through grant BB/F0202281, as well as by the number of industrial users. CCP4 6.3.0 is out now, and we hope that you will find it a helpful advance in crystallographic computing. Best wishes, CCP4 Core Team -- Scanned by iCritical.

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Van der waals interaction in phenix
by subhash bihani 16 Jul '12

16 Jul '12

Hi all, In one of my structure I have to put some water molecule in alternate confimation with amino acid residues and in another case with ligand. How do I do it in Phenix. Regards -- Subhash Bihani Scientific Officer Solid State Physics Division Bhabha Atomic Research Centre Trombay, Mumbai-85 Ph. 25594688 (o) alternate email: subhashbihani(a)yahoo.co.in

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default treatment of Intensities and structure factors in phenix.refine
by Yarrow Madrona 16 Jul '12

16 Jul '12

Hi, I recently noticed from reviewing the phenix.refine log file that phenix is scaling the input intensities using the French-Wilson Method. However, I have already run Truncate in CCP4 and have structure factors in my MTZ. So it appears that Phenix.refine ignores structure factors and uses intensities regardless. The reason I am concerned is that Nat recently mentioned that the default for the sigma I cutoff is zero. However, The default in Truncate I thought was -3. If I understand correctly, the treatment in truncate allows weak reflections to be scaled and converted to structure factors. It seems that setting the I sigma cutoff to zero would cause you to loose some useable data. Currently, the sigma_fobs_rejection_criterion and sigma_ibos_rejection_criterion = None. This is the default I guess which would be 0. So my questions are: 1. Will setting: sigma_iobs_rejection_criterion = -3 result in Phenix using a sigma I cutoff of -3? 2. How do I tell phenix to use the structure factors created by Truncate? Thanks for your help. I apologize if I have some misconceptions as I am still relatively new to crystallography. -Yarrow -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697

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