- phenixbb - phenix-online.org

Phenix version 1.10 released
by Paul Adams 09 Sep '15

09 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 06 Sep '15

06 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 04 Sep '15

04 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 28 Aug '15

28 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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