- phenixbb - phenix-online.org

3rd Annual Conference on the Biological Applications of X-ray Free Electron Lasers - BioXFEL
by Edward Snell 16 Sep '15

16 Sep '15

Dear all, This is not a directly related Phenix topic but the meeting may be of interest to Phenix users. Please note that the announcement also appeared on the CCP4 bulletin board with some incorrect spellings of names. I apologize to those concerned - my fault completely with travel, a high resolution laptop screen, and discovering I now need glasses to read at that resolution all to blame. The 3rd Annual Biological Applications of X-ray Free Electron Lasers (BioXFEL) meeting will be held at the Intercontinental Hotel in San Juan, Puerto Rico, from Jan 13th to 15th 2016. The conference is supported as part of the National Science Foundations BioXFEL Science and Technology Center, a consortium of eight US institutions headed by Ed Lattman and John Spence. The conference will focus on new and developing methods and biological results from biological XFEL research. The last day will cover hybridized developments capturing the growing interplay between XFEL and synchrotron sources. Confirmed speakers include Henry Chapman, Vadim Cherezov, Guillermo Calero, Marco Cammarata, Bob Fischetti, Helen Ginn, Heinz Graafsma, Abbas Ourmazd, Ilme Schlichting, Joerg Standfuss, and Rachel Woldeyes. Many others along with the preliminary agenda are to be announced shortly. The meeting will include education opportunities for post-doctoral and graduate students and an education and diversity talk by Cathy Drennan. A poster session will be held and a selection of abstracts submitted will be selected to be presented orally. The previous meeting of the series attracted over 150 international attendees with the talks, schedule, and environment stimulating much discussion and resulting in new collaborations. A diverse mixture of investigators from academic, industry and national laboratories will be present along with post-doctoral and graduate students. Anyone with an interest in this rapidly moving field is invited to attend. The registration fee is $300 (or $200 for students) with registration and details at https://www.bioxfel.org/events/details/64. Poster abstracts (with a preference for giving a talk if selected) should follow the format described on the webpage and be submitted by email to euppington(a)hwi.buffalo.edu. While the registration deadline is November 15th, the poster deadline is later, December 15th. However, talks will be selected from posters submitted from now until the registration deadline, until the presentation slots are filled. If you know of others who may not read the CCP4 board, please pass this information along. Come join us for a scientifically stimulating conference in a productive setting. Sincerely, Edward Snell and George Phillips (BioXFEL 2016 chairs) Edward Snell Ph.D. CEO Hauptman-Woodward Medical Research Institute Assistant Prof. Department of Structural Biology, SUNY Buffalo 700 Ellicott Street, Buffalo, NY 14203-1102 Phone: (716) 898 8631 Fax: (716) 898 8660 Skype: eddie.snell Email: esnell(a)hwi.buffalo.edu Heisenberg was probably here!

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2016 MicroED workshop at Janelia Research Campus
by Hattne, Johan 16 Sep '15

16 Sep '15

Janelia Research Campus (Ashburn, VA) will run a MicroED workshop February 22-25, 2016, hosted by Tamir Gonen. MicroED is a technique that uses electron diffraction to facilitate structure determination from sub-micron sized crystals, eliminating the need to grow large crystals. MicroED uses equipment and procedures that are standard on many cryo-TEM:s, and because of this the technique can be easily adopted in labs and facilities around the world. To encourage the widespread use of MicroED we are offering this workshop to teach microscopists how to perform the technique and adopt it at their own institutions. There is no registration fee for participation, and Janelia will provide on-site housing and meals. Attendees are expected to cover their own travel expenses and must be able to stay for the duration. Space in the course is limited. Those interested should send a brief statement on why they wish to participate to conference(a)janelia.hhmi.org by Friday, October 18. // Best wishes; Johan, on the behalf of the organizers Research Specialist @ Gonen Lab ____________________________________________________ Janelia Research Campus * 19700 Helix Drive Ashburn, VA 20147 * +1 (571) 209-4000 extension 3376

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Re: [phenixbb] refining different enantiomers
by Joel Tyndall 13 Sep '15

13 Sep '15

Hi all, Just an update on the solution (which was to use the altloc). I needed to use a different residue numbers as well as different names all with an altloc flag e.g. AABA B 1 BABB B 2 CABC B 3 etc This way they were all recognised and were all maintained as different molecules with differing stereochemistry Thanks to all who gave help J From: Phan, Jason [mailto:[email protected]] Sent: Friday, 11 September 2015 8:05 a.m. To: Joel Tyndall <joel.tyndall(a)otago.ac.nz> Subject: Re: [phenixbb] refining different enantiomers J, I’d give it the same res num and chain id so the program won’t treat them as different residues. Don’t for get the altloc (AS3L and BS3L in my case). HETATM 1467 S19AS3L A 204 -5.833 10.423 7.671 0.62 23.15 S HETATM 1468 N20AS3L A 204 -3.414 9.416 7.552 0.62 24.27 N HETATM 1469 C21AS3L A 204 -3.040 10.374 10.388 0.62 29.37 C HETATM 1470 N22AS3L A 204 -2.138 10.275 11.024 0.62 30.28 N HETATM 1471 N01BS3L A 204 -4.128 11.351 13.823 0.38 32.89 N HETATM 1472 C02BS3L A 204 -4.731 10.188 13.418 0.38 32.83 C HETATM 1473 O03BS3L A 204 -4.635 9.141 14.001 0.38 34.60 O HETATM 1474 O04BS3L A 204 -5.450 10.323 12.316 0.38 28.92 O Jason On Sep 10, 2015, at 12:02 AM, Joel Tyndall <joel.tyndall(a)otago.ac.nz<mailto:[email protected]>> wrote: Hi all, I have a case where we have crystallised a ligand in our protein and the ligand purchased is a mixture of 4 structural isomers (enantiomers and diastereomers). There is no way of telling if one over the other is bound in the active site so we have assumed all 4 are binding. I have generated 4 separate ligands with 4 separate cifs and the all fit the density. I am refining the complex with all 4 ligands at 0.25 occupancy (occupancy refinement is switched off, I have changed the clash guard non-bonded distance threshold is set to 0.0 (as an initial error message came up with nonbonded interactions < 0.5). My refinement ran to completion, but something is definitely not right. The pdb file won’t load in Coot and in pymol the ligands have imploded/exploded. I am just wondering if this is the best way to refine this structure (or I have missed something) and probably more to the point what have I missed with the ligands. To me it is almost identical to alternate conformations, but I have obviously missed something I have just install phenix 1.10 on a windows machine. Thanks J _________________________________ Joel Tyndall, PhD Associate Professor in Medicinal Chemistry National School of Pharmacy University of Otago PO Box 56 Dunedin 9054 New Zealand Skype: jtyndall Ph: +64 3 479 7293 _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org<mailto:[email protected]> http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: phenixbb-leave(a)phenix-online.org<mailto:[email protected]>

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Problem with mr_rosetta
by Kerff Fred 10 Sep '15

10 Sep '15

Hello, I’m trying to use mr_rosetta on my protein. I’m using OS X and upgraded phenix a couple of days ago and install rosetta at the same time. My job stops with the following message in this log file /phenix/MR_ROSETTA_52/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1/RUN_6/WORK_1/rebuild.log. ERROR: can't find residue type at pos 1 in sequence ...sequence removed… ERROR:: Exit from: src/core/pose/annotated_sequence.cc line: 236 [35m0 mr_protocols.macosclangrelease 0x000000010b198bd6 print_backtrace() + 54 1 mr_protocols.macosclangrelease 0x000000010b198ab4 utility::exit(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, int, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, int) + 804 2 mr_protocols.macosclangrelease 0x000000010a9b8ca1 core::pose::residue_types_from_sequence(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, core::chemical::ResidueTypeSet const&, bool) + 3697 3 mr_protocols.macosclangrelease 0x000000010a9ba6ea core::pose::make_pose_from_sequence(core::pose::Pose&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, core::chemical::ResidueTypeSet const&, bool) + 26 4 mr_protocols.macosclangrelease 0x0000000109267969 protocols::comparative_modeling::ThreadingJobInputter::pose_from_job(core::pose::Pose&, std::__1::shared_ptr<protocols::jd2::Job>) + 1449 5 mr_protocols.macosclangrelease 0x0000000109cb0c58 protocols::jd2::JobDistributor::run_one_job(std::__1::shared_ptr<protocols::moves::Mover>&, long, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, unsigned long&, unsigned long&, bool) + 2232 6 mr_protocols.macosclangrelease 0x0000000109cafb5b protocols::jd2::JobDistributor::go_main(std::__1::shared_ptr<protocols::moves::Mover>) + 331 7 mr_protocols.macosclangrelease 0x0000000109c8d1f2 protocols::jd2::FileSystemJobDistributor::go(std::__1::shared_ptr<protocols::moves::Mover>) + 66 8 mr_protocols.macosclangrelease 0x00000001089e9964 my_main(void*) + 3124 9 mr_protocols.macosclangrelease 0x00000001089eae19 main + 4713 10 libdyld.dylib 0x00007fff8c8555c9 start + 1 11 ??? 0x0000000000000002 0x0 + 2 [0mError: ERROR: Exception caught by JobDistributor while trying to get pose from job 'S_PHENI_0001' Error: [ERROR] EXCN_utility_exit has been thrown from: src/core/pose/annotated_sequence.cc line: 236 ERROR: can't find residue type at pos 1 in sequence ...sequence removed... Error: Treating failure as bad input; canceling similar jobs protocols.jd2.FileSystemJobDistributor: job failed, reporting bad input; other jobs of same input will be canceled: S_PHENI_0001 protocols.jd2.JobDistributor: no more batches to process... protocols.jd2.JobDistributor: 15 jobs considered, 1 jobs attempted in 0 seconds caught exception 1 jobs failed; check output for error messages Anybody can help? Thanks Fred ----- Frédéric Kerff Chercheur qualifié F.R.S.-FNRS Cristallographie des protéines Centre d'Ingénierie des Protéines Université de Liège 17, Allée du 6 Août - Bat B5a 4000 Liège (Belgium) Tel.: +32 (0)4 3663620 Fax: +32 (0)4 3663772

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refining different enantiomers
by Joel Tyndall 10 Sep '15

10 Sep '15

Hi all, I have a case where we have crystallised a ligand in our protein and the ligand purchased is a mixture of 4 structural isomers (enantiomers and diastereomers). There is no way of telling if one over the other is bound in the active site so we have assumed all 4 are binding. I have generated 4 separate ligands with 4 separate cifs and the all fit the density. I am refining the complex with all 4 ligands at 0.25 occupancy (occupancy refinement is switched off, I have changed the clash guard non-bonded distance threshold is set to 0.0 (as an initial error message came up with nonbonded interactions < 0.5). My refinement ran to completion, but something is definitely not right. The pdb file won't load in Coot and in pymol the ligands have imploded/exploded. I am just wondering if this is the best way to refine this structure (or I have missed something) and probably more to the point what have I missed with the ligands. To me it is almost identical to alternate conformations, but I have obviously missed something I have just install phenix 1.10 on a windows machine. Thanks J _________________________________ Joel Tyndall, PhD Associate Professor in Medicinal Chemistry National School of Pharmacy University of Otago PO Box 56 Dunedin 9054 New Zealand Skype: jtyndall Ph: +64 3 479 7293

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Phenix version 1.10 released
by Paul Adams 08 Sep '15

08 Sep '15

The Phenix developers are pleased to announce that version 1.10 of Phenix is now available (build 1.10-2155). Binary installers for Linux, Mac OSX, and Windows platforms are available at the download site: http://phenix-online.org/download/ Highlights for this version: CDL as the default protein restraints, tools for planning a SAD experiment and scaling/merging SAD data, refactored xtriage GUI, use of intensities in molecular replacement, occupancy refinement mode after MR to automatically prune the model, expanded real space refinement for cryo-EM (and X-ray) data, NCS constraints in refinement, improved rotamer fitting in refinement, improved and consolidated secondary structure restraints, validation of peptide planes, protein backbone validation using Cablam, structure search tool, updated feature enhanced map protocol, TLS analysis tools, new continuous integration build system (BuildBot), and many other new utilities and fixes. General: ======== - New continuous build system, Buildbot - New tools for planning and evaluating SAD data collection and SAD datasets - All command-line installers converted to Python - Removed dependency on Apple tools for Mac installer relocation - Improved geometry restraints: - Nucleic acids: basepair planarity, hydrogen bonding and stacking restraints - Angle and torsion restraints for disulfide bonds - Conformation-Dependent Library is now the default (cdl=True) - Automatic linking has been expanded with carbohydrate linking being the default in all applicable programs - Names and places of parameters controlling secondary structure, reference and NCS restraints were changed - NCS constraints ("strict" NCS) for refinement (phenix.refine and phenix.real_space_refine) - Applied to coordinates and ADPs - Option to refine NCS operators - Partial LINK records support: - only in phenix.refine, phenix.geometry_minimization & phenix.real_space_refine - output LINK records generated using automatic linking and applied .edits (LINK in input PDB file are ignored) - HELIX/SHEET records in input file will be preserved in output PDB file Graphical interface: ==================== - Integrated help browser now supported on Linux - Improved display of Xtriage results, with summary of problems with data - Support for 'within' syntax in graphical atom selections - Model Reconstruction GUI: new GUI for building complete asymmetric unit and biological molecules using MTRIX and BIOMT records, respectively, in the PDB file - New interface for phenix.anomalous_signal - New interface for phenix.scale_and_merge Refinement: =========== - phenix.refine - Optionally use AFITT for geometry restraints of ligands - mmCIF output now includes _refln.pdbx_r_free_flag tag to explicitly record original R-free flags (instead of implicitly in status tag) - Updated Phenix GUI to handle reorganization of NCS implementation - main.secondary_structure_restraints, main.ncs and main.reference_model_restraints parameters were removed - Improved rotamer fitting (faster, less outliers) - Bug fixes - phenix.real_space_refine: - rigid-body refinement with possibility to specify rigid groups - NCS constraints are used by default - NCS groups are found automatically, also can be specified manually - support for custom restraints - support for ligand CIF files - map can have any origin (non-zero), refined model is not shifted to zero origin - if CCP4 map is used resolution must be specified using “resolution" keyword - Enable reference model restraints, including restraining to self - Many bug fixes, many tests added - phenix.secondary_structure_restraints (proteins and DNA/RNA) - Three methods are available to annotate protein secondary structure - Protein secondary structure definition may be outputted as HELIX/SHEET records in PDB format - New algorithm to search for nucleic acid base pairs and stacked pairs. - phenix.rosetta_refine: - more options for map type for real-space refinement, including composit omit and feature-enhanced maps - partial support for ligands (requires separate parameter files) - phenix.tls_analysis: - Decomposition of TLS matrices into elemental rigid-body motions (axes and amplitudes of vibration and libration). Validate TLS matrices. - phenix.tls_as_xyz: - Explicit interpretation of refined TLS parameters by decomposing into elemental rigid-body motions and generating structural ensembles that are consistent with these motions - phenix.multistart_sa: - utility for running multi-start simulated annealing refinements with varying random seed - sample uncertainty due to stochastic effects - also performs map averaging - parallelizes across multicore systems or managed clusters Experimental Phasing and Model Building: ======================================== - phenix.xtriage: - refactored for greater modularity and consistency between command line and Phenix GUI - simplified and clarified feedback, including new summary panel - many bug and stability fixes from PDB-wide testing - detection of elliptical truncation - analyze completeness of anomalous vs non-anomalous dataset - phenix.plan_sad_experiment (new command, GUI and command-line): - Estimate the I/sigI for a dataset that will be necessary to solve a structure by SAD - phenix.scale_and_merge (new command, GUI and command-line): - scale one or more SAD datasets, optimally using unmerged original index data, to create a scaled, merged dataset and to estimate the half-dataset anomalous correlation - phenix.get_cc_ano (new command,command-line only): - Calculate the anomalous correlation between two datasets - phenix.get_patterson_skew (new command, command-line only): - Get the skew of an anomalous difference Patterson and the ratio of anomalous differences to anomalous error. - phenix.merging_statistics: - calculate CC(anom) for split half-datasets Molecular Replacement: ====================== - Phaser: - now allows direct use of intensities instead of amplitudes for molecular replacement - new treatment of effect of intensity measurement error introduced - improved handling of weak data in normalization and anisotropy correction - new occupancy refinement mode to retain or prune residues along a chain - highlights loops and domains that are likely to need major correction - automatically invoked if high TFZ-score solution rejected for bad packing - subgroups feature: Phaser lists possible subgroups of space group, and if twinning is suspected the space group can be set explicitly to one of its subgroups for a molecular replacement search. In this case, the data will be expanded to the unique set for the subgroup. - new "Search" panel GUI making it less confusing to define multicomponent searches - replacing "Composition" with "ASU contents" on the GUI - phased translation function can be used, even as part of MR_AUTO search - magnification factor (cell scale) can be refined for electron density as a model: useful when cryoEM image reconstructions serve as models - SAD likelihood now reported as log-likelihood-gain: positive number relative to null hypothesis - Phaser now prints out suggestion for number of copies related by successive application of NCS translations (TNCS NMOL parameter), if suggested value > 2 - fixed bug affecting xyz-values > 100 in PDB for substructure - various other bug fixes - phenix.find_alt_orig_sym_mate: - Created new alias, phenix.famos, which is an anagram of the acronym for find_alt_orig_sym_mate and is easier to remember for the commandline. - phenix.subgroup_symmetry_datasets: - Calculates all subgroup of the diffraction data, and outputs them on the conventional setting. Useful to explore options when multple twin laws are possible. - phenix.structural_domain_search: - Domain search program using an approach based on graph theory. Very quick and fairly accurate for simple problems. Validation: =========== - phenix.omegalyze: - Identify non-trans peptide bonds in proteins. Three categories of peptide bond geometry: trans, cis, and twisted (>30deg away from planar). - phenix.cablam_validate: - Validation of protein backbones now uses separate contours for trans-proline vs cis-proline. - phenix.molprobity: - incorporated RNA validation New commands: ============= - phenix.model_idealization (new command, command-line only): - phenix.plan_sad_experiment (new command, GUI and command-line): - phenix.scale_and_merge (new command, GUI and command-line): - phenix.get_cc_ano (new command,command-line only): - phenix.get_patterson_skew (new command, command-line only): Other: ====== - phenix.model_idealization (new command, command-line only): - Idealize geometry of the input model. Only secondary structure elements of proteins are currently supported. - phenix.structure_search Quickly find homologous structures for a given model. There is an option to compile and output a list of ligands found in structures of those homologs. - phenix.map_model_cc (and its synonym phenix.model_map_cc): Compute model-map correlation coefficient (map CC or RSCC). Output overall, per whole model, per chain and per residue CC. Input map needs to be CCP4 fromatted file. - phenix.fem: - various bug fixes - make using "maximal synthesis" the default (before "minimal synthesis" was the default) - current version obsoletes all previous versions - phenix.chains_as_models: Convert PDB file with multiple chains into PDB file with multiple models (MODEL-ENDMDL). - phenix.models_as_chains: Convert multi-model (MODEL-ENDMDL) file into one model file with each model assigned unique chain ID. - phenix.helix_sheet_recs_as_pdb_files: Split PDB file into several PDB files with each file representing HELIX or SHEET record found in PDB file header. - phenix.map_value_at_point: Output map values at specified (x,y,z) points in space. - phenix.map_box: Extract box around selected atoms with map. Output PDB with atoms in the box and map files in CCP4, X-plor and MTZ formats. - phenix.model_model_distances: Given two PDB files output distances per atom, residue, chain, model and overall. It is assumed (and asserted in the code!) that the amount and order of atoms in both files are identical. - phenix.simple_ncs_from_pdb: Tool to find NCS groups in PDB model. Available in previous versions. Major code re-write to improve re-usabiliy. For a full list of changes see: http://www.phenix-online.org/documentation/CHANGES Please note that this publication should be used to cite use of Phenix: PHENIX: a comprehensive Python-based system for macromolecular structure solution. P. D. Adams, P. V. Afonine, G. Bunkóczi, V. B. Chen, I. W. Davis, N. Echols, J. J. Headd, L.-W. Hung, G. J. Kapral, R. W. Grosse-Kunstleve, A. J. McCoy, N. W. Moriarty, R. Oeffner, R. J. Read, D. C. Richardson, J. S. Richardson, T. C. Terwilliger and P. H. Zwart. Acta Cryst. D66, 213-221 (2010). Full documentation is available here: http://www.phenix-online.org/documentation/ There is a Phenix bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb/ Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: help(a)phenix-online.org and bugs(a)phenix-online.org Commercial users interested in obtaining access to Phenix should visit the Phenix website for information about the Phenix Industrial Consortium. The development of Phenix is principally funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Laboratory Research Manager, ENIGMA Science Focus Area Building 33, Room 347 Building 80, Room 247 Building 978, Room 4126 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ LBenvenue(a)lbl.gov ][ 1-510-495-2506 ] --

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on "occupancies" in the phenix.refine GUI
by Smith Liu 07 Sep '15

07 Sep '15

Dear All, In my map for a specific HISresidue, it was rather clear the sidechain has 2 conformations. In my start modle, I only have the PDB for 1 of the 2 conformations of the sidechain. With "occupancies" clicked, the refined PDB still only contain the PDB for 1of the 2 conformations of the sidechain (occupancy is 1). Thus in order to have the GUI "occupancies" takes function, I need manually add the PDB for the conformation of the other side chain, am I right? If I am right，will you please show me an PDB example which contains the conformations for 2 or several sidechains of a residue, so that I can know how to edit this kind of PDB? Best regards. Smith

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Transfer FreeR and FreeR test set flag value
by Matthew Chu 07 Sep '15

07 Sep '15

Dear All, I am trying to refine my model against a higher resolution dataset. My colleage's old-low resolution dataset was processed in HKL/scalepack and the FreeR was assigned by Phenix.reflection file editor, which I assume the test set was marked as "1". Now I got a new-higher resolution dataset, and plan to process it in XDS/Aimless. I want to transfer the FreeR set from his old mtz and also use his low res model for the new refinement. My question is, when I transfer the FreeR set from his old mtz with flag value as "1" in Aimless, is the flag value now "1" or "0" in the new mtz output by Aimless? Can Aimless recognize the FreeR flag from the old mtz which are marked as "1"? I also read an old post from Nat Echols in 2011: "For Phenix, 1 is test, 0 is work, but you could reverse this and it will still figure out what to do automatically", so does it mean it doesn't matter if the FreeR is "1" or "0" in the mtz from Aimless, if I use phenix.refine for my new dataset, Phenix can figure out which is the correct FreeR value? It's a mix of CCP4 and Phenix question, so I have crossed posted it in the CCP4bb as well. Many thanks, Matt

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a question on phenix refine
by Smith Liu 05 Sep '15

05 Sep '15

Dear All, For the GUI of phenix.refine, if we click "Optimize X-ray/stereochemistry weight", it should optimize on how to part the weight between X-ray and stereochemistry. Then if we do not click "Optimize X-ray/stereochemistry weight", phenix.refine will do with whole weight from "X-ray" or whole weight from "stereochemistry"? I am looking forward to getting your reply. Smith

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Space group
by mohamed noor 04 Sep '15

04 Sep '15

Dear all I processed my images in point group P 3 2 1. After running Phaser and building it, the space group was P 3(2) 2 1. However, the refinement is stuck with Rfree at around 35-38 % (data extending to 3.3 A). As I believe the R factor is a bit high, and I have a different crystal form in P4(2) 2(1) 2 with R free at 25 % for data to 3.8 A, I expanded it to P 1, redid Phaser searching for 48 copies. After refinement, the R free is at 38 %. For some reason, Zanuda/Refmac is not able to read my files. So I ran Xtriage instead: A summary of R values for various possible point groups follow. ------------------------------------------------------------------------------------------------------- | Point group | mean R_used | max R_used | mean R_unused | min R_unused | BIC | choice | ------------------------------------------------------------------------------------------------------- | P 3 | 0.000 | 0.000 | 0.271 | 0.000 | 3.521e+05 | | | C 1 2 1 (2*y,-x+y,z) | 0.423 | 0.423 | 0.200 | 0.000 | 1.763e+06 | | | P 1 | None | None | 0.219 | 0.000 | 1.056e+06 | | | P 6 | 0.242 | 0.423 | 0.200 | 0.000 | 1.365e+06 | | | C 2 2 2 (x+y,2*y,z) | 0.271 | 0.423 | 0.200 | 0.000 | 1.464e+06 | | | P 3 2 1 | 0.000 | 0.000 | 0.423 | 0.423 | 1.761e+05 | | | P 3 1 2 | 0.242 | 0.423 | 0.200 | 0.000 | 1.365e+06 | | | C 2 2 2 (2*x,x+y,z) | 0.271 | 0.423 | 0.200 | 0.000 | 1.464e+06 | | | P 1 1 2 | 0.423 | 0.423 | 0.200 | 0.000 | 1.763e+06 | | | P 6 2 2 | 0.219 | 0.423 | None | None | 1.265e+06 | | | C 1 2 1 (x+y,-x+y,z) | 0.000 | 0.000 | 0.242 | 0.000 | 5.282e+05 | | | C 1 2 1 (x+y,2*y,z) | 0.423 | 0.423 | 0.200 | 0.000 | 1.763e+06 | | | C 1 2 1 (x-y,2*x,z) | 0.000 | 0.000 | 0.242 | 0.000 | 5.282e+05 | | | C 2 2 2 (x-y,x+y,z) | 0.271 | 0.423 | 0.200 | 0.000 | 1.464e+06 | | | C 1 2 1 (2*x,x+y,z) | 0.000 | 0.000 | 0.242 | 0.000 | 5.282e+05 | | | C 1 2 1 (x-y,x+y,z) | 0.423 | 0.423 | 0.200 | 0.000 | 1.763e+06 | | ------------------------------------------------------------------------------------------------------- R_used: mean and maximum R value for symmetry operators *used* in this point group R_unused: mean and minimum R value for symmetry operators *not used* in this point group Looking at the R values, it is possible that it is actually C 1 2 1. My questions: 1. What is the difference between the C 1 2 1 lines? What do the values in brackets mean? 2. Since Xtriage did indicate a possible NCS axis parallel to crystallographic axis (and it looks almost like that in my P321 model), do I reintegrate in one of those C121 and then redo Phaser/refinement? I can post a screenshot of model if that will help. Thanks. Mohamed

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Positive density at metal ions
by Jan van Agthoven 03 Sep '15

03 Sep '15

Hi everyone, I work on a structure of about 3 A resolution. The structure is almost done except for 3 metal ions which remain positive in the density. The metal is clearly Mn (refinement works fine for an other very similar structure) and has been set at full occupancy. I tried to reset the B factor at lower values, which solves the problem for 2 metal ions but not the 3rd one. Is there anything else I can do? Jan

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Rwork higher than Rfree
by Smith Liu 01 Sep '15

01 Sep '15

Dear All, Is poor resolution a factor leading to Rwork higher than Rfree? Any other factor? Best regards. Smith

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Cell dimentions
by Bradley Hintze 30 Aug '15

30 Aug '15

Hello I have some interesting DNA structures I would like help with . The duplexes are stacked in the crystal head to head and tail to tail. This creates an interesting situation where an adenine is base pairing with itself across cell symmetry. The most likely way in which adenines base pairs with itself is if one is in the syn conformation and the other is in anti, i.e. a Hoogsteen base pair. However, that would break the symmetry as they are the same adenine and thus can't have two conformations. As such, I think it's appropriate to have two molecules, rather than one, in the asymmetric unit. I can make the new model easily enough by generating a symmetry mate and assigning different chain IDs but how do I appropriately calculate the new cell dimensions? Thanks, Bradley

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on phenix refine of the cryo-EM data
by Smith Liu 29 Aug '15

29 Aug '15

Dear All, Phenix.real_space_refine can give nice results, but I still want to refine it by phenix refine graphical interface so that the refined PDB by Phenix.real_space_refine can have a much better resolution PDB from crystal structure as a reference PDB for further refine by phenix refine GUI, in case a fragment of the sequence may adopt a sheet structure as the reference structure, rather than a loop structure as obtained by Phenix.real_space_refine. When I use the phenix refine GUI for further refine, do I need to use electron scattering table, or I continue to use n-Gaussian scattering table? For the phenix refine GUI for this purpose, there will ne no necessity to click Optimized X-ray/sterochemistry weight and Optimize X-ray/ADP weight, as for it has no relationship with X-ray, am I right? The phenix.map_to_structure_factors converted mtz file, should correspond to the 2FoFcWT file. In the phenix GUI refine process, it will calculate the FoFcWT file. But each time I tried the refine by phenix GUI related to phenix.map_to_structure_factors converted mtz file, the signal of the FoFcWT file was almost as strong as or even much stronger than the 2FoFcWT file, which was in strong contrast with the phenix refine based on the crystal mtz file. Will you please explain why for phenix.map_to_structure_factors converted mtz file, phenix GUI can give such high signal of FoFcWT file? Best regards. Smith

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off-topic: tenure track faculty position in cryo-EM
by Markus Seeliger 27 Aug '15

27 Aug '15

*Department of Pharmacological Sciences at **Stony Brook University * *Tenure-Track Cryo-EM Faculty Position in Conjunction with the Interdisciplinary Biomolecular Imaging Cluster Hiring Initiative* The Department of Pharmacological Sciences ( http://www.pharm.stonybrook.edu/faculty_research/overview) at Stony Brook University seeks applications for a tenure-track faculty position at the level of Assistant, Associate, or Full Professor. Candidates must have an M.D. and/or Ph.D., at least two years of postgraduate research experience, and an outstanding record of research accomplishment. This search is intended to recruit investigators with translational research programs that make use of Cryo-EM to pursue fundamental questions relevant to health-connected fields such as cancer, neuroscience, metabolism, and infectious disease. Senior candidates should have a record of success with extramural funding and training of students and/or fellows. Applicants must be eligible for a faculty appointment in accordance with the criteria established by the School of Medicine (Criteria for Appointment, Promotion and Tenure.) The Department has pre-doctoral and MSTP training grants, a broad infrastructure for research investigation, and newly renovated lab space housing structural biologists with expertise in NMR and x-ray crystallography. Many of the faculty use EM and Super-Resolution microscopy approaches, and additional structural biologists and imagers are found in the Departments of Biochemistry, Physiology, Chemistry, Microbiology, Neurobiology, and Biomedical Engineering. With the on-going NYSUNY 2020 Challenge Grant awarded to the University and the recent and largest gift ever to public higher education in the State of New York, Stony Brook University is embarking on a transformational expansion of the biomedical research enterprise. Diverse opportunities for collaborative research on campus include the Cancer Center, the Laufer Center for Physical and Quantitative Biology, the Center for Structural Biology, the Institute for Chemical Biology and Drug Discovery, and the interactive Computer Science and Applied Mathematics Departments. Imaging biological molecules is key to understanding their function, providing a starting point for rational drug design and protein engineering. Stony Brook University (SBU) is becoming a leader in biomolecular imaging through its newly-upgraded high-field NMR facilities including Bruker 700MHz and 850 MHz instruments with cryogenic probes, a strong program in computational structural and physical biology, world-class computational resources, facilities for radiotracer synthesis and human imaging, and proximity to the new third- generation synchrotron facility at Brookhaven National Lab (NSLS-II). The Biomolecular Imaging Cluster has already recruited junior faculty with expertise in x-ray crystallography and in super-resolution microscopy to add to our recent NIH-funded purchase of SIM and STORM instrumentation. *Most relevant to this recruitment, SBU received this year a $2M Shared Instrumentation award from NIH to obtain a state-of-the-art 200 kV Talos cryo-EM microscope and detector that will be installed and go live in Spring, 2016. * Stony Brook University, home to many highly-ranked graduate research programs, is located 60 miles from New York City on Long Island's scenic North Shore. Our 1,100-acre campus has more than 24,000 undergraduate, graduate, and doctoral students and 13,500 faculty and staff. The University is a member of the prestigious Association of American Universities and co-manager of the nearby Brookhaven National Laboratory, a multidisciplinary research laboratory supporting world-class scientific programs utilizing state-of- the-art facilities. Stony Brook University is also located close to the Cold Spring Harbor Laboratory with which it interacts through graduate program training and faculty collaborations. To apply, use Academic Jobs Online ( https://academicjobsonline.org/ajo/jobs/5904) to submit a State employment application, a complete curriculum vitae including publications, and a 3-page proposed research plan of current and future research, and have three letters of recommendation submitted through the AJO site. The cover letter should indicate whether the applicant wishes to be considered for appointment at the Assistant, Associate, or Full Professor level. Applicants at the Associate or Full Professor level should add a summary of past and current research funding and administrative and teaching experiences. *Electronic submission through AJO is required.* Questions should be addressed to Ms. Lynda Perdomo-Ayala, Department Administrator ( lynda.perdomo-ayala(a)stonybrook.edu, fax (631-444-9749.) POSITION OPEN UNTIL FILLED. For a full position description, visit www.stonybrook.edu/jobs (Ref.F-9530/15/08). Stony Brook University is an Affirmative Action, Equal Opportunity Educator and Employer.

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Re: [phenixbb] phenixbb Digest, Vol 117, Issue 9
by Cesar Santiago 27 Aug '15

27 Aug '15

Hi Mark! Anybody for the 24th trip to Alba? I'll be away from the 1st - 16th of September but I can still arrange the trip before leaving. César. ------------------------------------------------------------------ Cesar Santiago, Ph. D. Dept. of Macromolecules Structure at CNB, CSIC. X-ray Crystallography Facility. Campus Universidad Autónoma. Madrid, 28049 csantiag(a)cnb.csic.es On Aug 27, 2015, at 6:42 AM, phenixbb-request(a)phenix-online.org wrote: > Send phenixbb mailing list submissions to > phenixbb(a)phenix-online.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://phenix-online.org/mailman/listinfo/phenixbb > or, via email, send a message with subject or body 'help' to > phenixbb-request(a)phenix-online.org > > You can reach the person managing the list at > phenixbb-owner(a)phenix-online.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of phenixbb digest..." > > > Today's Topics: > > 1. Re: phenix.refine automatic linking options (Engin ?zkan) > 2. external passive 3D monitor with macbook pro or imac for coot > and pymol stereo view (Xiao Lei) > 3. Rank-scaled map (Jianghai Zhu) > 4. Re: Rank-scaled map (Pavel Afonine) > 5. Re: on the starting mtz file for phenix refine (Pavel Afonine) > 6. Ligand addition in COOT for later refinement in Phenix.refine > (Manoj saxena) > 7. Re: Ligand addition in COOT for later refinement in > Phenix.refine (Oleg Sobolev) > 8. Computational Crystallography Newsletter - Volume 6, Number 2 > (Nigel Moriarty) > 9. Starting structure as reference model - crashing in 1.10-2142 > (Tristan Croll) > 10. Re: Starting structure as reference model - crashing in > 1.10-2142 (Pavel Afonine) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 20 Aug 2015 15:41:31 -0500 > From: Engin ?zkan <eozkan(a)uchicago.edu> > To: Billy Poon <bkpoon(a)lbl.gov> > Cc: PHENIX user mailing list <phenixbb(a)phenix-online.org> > Subject: Re: [phenixbb] phenix.refine automatic linking options > Message-ID: <55D63B7B.6000707(a)uchicago.edu> > Content-Type: text/plain; charset="utf-8"; Format="flowed" > > Dear Billy and Nigel, > > Thank you. Phenix.refine GUI in the latest nightly/release candidate no > longer has the master enable/disable button, and so the problem is resolved. > > Engin > > On 8/13/15 11:28 AM, Billy Poon wrote: >> Hi Engin, >> >> Thanks! We updated that part of the GUI so that it should be more >> intuitive. There is now a button that lets you apply automatic linking >> to all the components and a button that disables all automatic >> linking. You can, of course, still pick which components to enable by >> checking the specific boxes. >> >> On Tue, Aug 11, 2015 at 7:40 AM, Engin ?zkan <eozkan(a)uchicago.edu >> <mailto:[email protected]>> wrote: >> >> Dear Developers, >> >> Using the latest phenix nightly, I observed something odd in the >> phenix.refine UI, and I thought I should report it. If one >> unchecks Automatic ligand linking, this seems to not override its >> options, as the instructions in the Options window suggest. >> Specifically, if "Automatic Ligand Linking" is unchecked, but the >> "Link metals" is checked within its Options window, metal link >> restraints are still created. >> >> I checked the .geo file to confirm this. >> >> Thanks, >> Engin >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org <mailto:[email protected]> >> http://phenix-online.org/mailman/listinfo/phenixbb >> Unsubscribe: phenixbb-leave(a)phenix-online.org >> <mailto:[email protected]> >> >> >> > >

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Starting structure as reference model - crashing in 1.10-2142
by Tristan Croll 27 Aug '15

27 Aug '15

Hi, When I attempt to run a refinement in Phenix 1.10-2142 using the starting structure as a reference model, it crashes with the complaint that the reference (actually, the error states NCS - despite no NCS being present or enabled. I guess internally it's using the same code?) is too dissimilar to the model, and a calculated RMSD of >90 (degrees? I'm using torsion-angle restraints in any case). The same settings work without complaint on the same structure in dev-2006. I'm running from the GUI, checking "Reference model restraints" in the main phenix.refine window, and then "use starting model as reference" under "All parameters... Reference model restraints...". Thanks, Tristan

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Computational Crystallography Newsletter - Volume 6, Number 2
by Nigel Moriarty 25 Aug '15

25 Aug '15

I am pleased to announce the publication of the latest issue of the Computational Crystallography Newsletter: http://www.phenix-online.org/newsletter/ A listing of the articles and short communications is given below. Please note that the newsletter accepts articles of a general nature of interest to all crystallographers. Please send any articles to me at NWMoriarty(a)lbl.gov noting that there is a Word Template on the website to streamline production. July 2015 <http://www.phenix-online.org/newsletter/CCN_2015_07.pdf> Articles - A context-sensitive guide to RNA & DNA base-pair & base-stack geometry <http://www.phenix-online.org/newsletter/CCN_2015_07.pdf#page=22> Short Communications - New Phaser-MR search panel in Phenix <http://www.phenix-online.org/newsletter/CCN_2015_07.pdf#page=7> - Quantum chemical techniques for minimising ligand geometries in the active site <http://www.phenix-online.org/newsletter/CCN_2015_07.pdf#page=10> - 13 typical occupancy refinement scenarios and available options in *phenix.refine* <http://www.phenix-online.org/newsletter/CCN_2015_07.pdf#page=12> Fitting tips #10 – How do your base pairs touch and twist? <http://www.phenix-online.org/newsletter/CCN_2015_07.pdf#page=3> Cheers Nigel --- Nigel W. Moriarty Building 33R0349, 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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Ligand addition in COOT for later refinement in Phenix.refine
by Manoj saxena 24 Aug '15

24 Aug '15

Greetings I am trying to place a ligand (CIT) in a protein model that already have some citrate ligands placed. I am doing this using Coot's option "get monomer", and after the fitting of ligand in the density I tried to refine the model using the ligand and the protein pdb as input models. Refinement did not start and I got an error message in Phenix- "Number of groups of duplicate atom labels:....." Could someone please explain how could I get past this error message and what is the correct way to add a ligand to a model that already has some of the ligands of the same type. Many thanks in advance Regards Manoj Saxena

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on the starting mtz file for phenix refine
by Smith Lee 22 Aug '15

22 Aug '15

Dear All, In the on-line phenix document, there is, "Should I use the MTZ file output by phenix.refine as input for the next round of refinement? The only time this is necessary is when you refined against a dataset that did not include R-free flags, and let phenix.refine generate a new test set. In this case, you should use the file ending in "_data.mtz" for all future rounds of refinement. You do not need to update the input file in each round, as the actual raw data (and R-free flags) are not modified". When we have phenic adding R-free flgas in the first time we process the mtz data by phenix.refine, besides the *data.mtz, phenix also create a *.mtz. In the future phenix.refine, can I refine by always using the *.mtz created in the R-free flag adding step, rather than refine by always using the *data.mtz created in the R-free flag adding step? What is the difference between that *data.mtz and that *.mtz? And what is the side-effect if in the future steps I refine by always using the *.mtz created in the R-free flag adding step? Best regards. Smith

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Rank-scaled map
by Jianghai Zhu 21 Aug '15

21 Aug '15

Hi, I know PHENIX can calculate a rank-scaled density map. Could anyone inform me which program in PHENIX actually does this? Thanks. Best, --Jianghai

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external passive 3D monitor with macbook pro or imac for coot and pymol stereo view
by Xiao Lei 21 Aug '15

21 Aug '15

Dear phenixbb members, I'm thinking to view stereo 3D structure on coot and pymol with passive 3D monitor, does anyone have experience of doing this with a macbook pro or imac and a external passive 3D monitor connected using HDMI port? If mac does not support this, should I buy a PC and a passive 3D monitor to do it? Thanks ahead. Xiao

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phenix.refine automatic linking options
by Engin Özkan 20 Aug '15

20 Aug '15

Dear Developers, Using the latest phenix nightly, I observed something odd in the phenix.refine UI, and I thought I should report it. If one unchecks Automatic ligand linking, this seems to not override its options, as the instructions in the Options window suggest. Specifically, if "Automatic Ligand Linking" is unchecked, but the "Link metals" is checked within its Options window, metal link restraints are still created. I checked the .geo file to confirm this. Thanks, Engin

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Phenix on Mageia
by Marie Elizabeth Fraser 19 Aug '15

19 Aug '15

Hello, We are having a problem getting the display of the cycles of Phenix running on our Linux machines. I am running Mageia 4, but the problem first appeared when I added a new student and he started to run Phenix on Mandriva. When I changed to Mageia 4, I had to do a clean install, so everyone got new home directories. Then the problem appeared for all of us. This has gone in as a bug report (and I can send the message if that would help). The response was that we were using a character like “é” in the filename or directory. I do not think that we are. However, at the bottom of the bug report it does say "LATIN CAPITAL LETTER A WITH RING ABOVE = Ã…”, which sounds like the symbol for Angstrom. Has anyone else seen a similar problem and been able to fix it? Thank you, Marie

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planarity between atoms of neighboring residues
by Agnieszka Kiliszek 19 Aug '15

19 Aug '15

Dear All, I would like to add restrains between two residues. I was trying to use geometry restrains planarity but I don't know how to select atoms from two different residues. I mean, I have: chain A resid 1 atoms: C5' C' and O1' chain A resid 2 atom: N1' I would like all 4 atoms to be planar. I found example only for atoms from the same residue. Can you help me? Agnieszka

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