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Worse R factor with newer version of phenix
by Jan van Agthoven 09 Oct '13

09 Oct '13

Hi everyone, I've been working on a low resolution structure (3.6A) which was previously refined with phenix 1.8_1069 (with a reference model, strategy=individual_sites,individual_adp ). I used the same input files and parameters and ended up with significantly different R factors. Start: r_work = 0.2850 r_free = 0.3189 bonds = 0.005 angles = 1.059 Final: r_work = 0.2609 r_free = 0.3160 bonds = 0.003 angles = 0.997 For the old version and Start: r_work = 0.2779 r_free = 0.3183 bonds = 0.006 angles = 1.141 Final: r_work = 0.2889 r_free = 0.3303 bonds = 0.021 angles = 2.737 with the new version 1.8.4 Remarkably it also came with an increased number of C-beta deviation (0 against 16!). Adding tls refinement or ramachandran restrains did not help. Now because I was using the .eff file of an old version of phenix, it came with a long list of unused parameters. These parameters however were all used by default. What should I do? Should I go back to this old phenix, or is there a way to improve the result? Thanks,

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Phenix version 1.8.4 released
by Paul Adams 09 Oct '13

09 Oct '13

The Phenix developers are pleased to announce that version 1.8.4 of Phenix is now available. Binary installers for Linux, Mac OSX, and Windows platforms are available at the download site: http://phenix-online.org/download/ Highlights from this version: Automated MR/ligand fitting/refinement pipeline (phenix.ligand_pipeline), improved determination of bulk solvent masks, improved real space refinement, GUI for ERRASER, improvements to AutoSol and AutoBuild, improvements to Phaser, improvements to Guided Ligand Replacement, 64-bit Windows 7 installer. Graphical interface: ==================== - New GUIs: ERRASER, phenix.dynamics - Pause/resume function for most programs on Mac/Linux - Utilities for conversion to/from mmCIF General: ======== - Multiple bug fixes - 64-bit Windows 7 installer - Improved bulk solvent mask calculations (phenix.refine, phenix.maps, etc.): - analyzes mFo-DFc map to identify spurious negative density blobs in bulk solvent regions and applies correction, can decrease R-factors by 0.5-2.0% Refinement: =========== - phenix.refine: - bug fixes in occupancy refinement, hydrogen addition - new local and global real-space refinement (RSR) methods: - Global RSR (refine all atoms, as before) runs only if: d_min > 1.5, r_work > 0.25, and not neutron data or "individual_sites_real_space" is the only selected strategy - Local RSR: residue-by-residue, replaces old fix_rotamers option - fits both main chain and sidechain - only applies to residues with rotamer outlier, poor CC, or clashes - new residue fit serves as torsion restrains for subsequent macro-cycle - normally not performed when explicit hydrogens present - added omit_selection keyword: sets atom occupancies for a selection to zero prior to refinement - optional harmonic restraints on starting positions - used to maintain structure close to starting model during simulated annealing omit map calculation - alpha feature: placement of elemental ions (place_ions=True) - looks for Mg, Cl, Ca, and Zn by default; specify elements=Cl,Ni,... to give explicit list (recommended) - works best with anomalous data Experimental Phasing and Model Building: ======================================== - AutoSol: - overall_best_refine_data.mtz now contains uncorrected F+,sigF+,F-,sigF- data and uncorrected FP,SIGFP. Previously only the FP,SIGFP was uncorrected, and F+,sigF+,F -,sigF- had been corrected for anisotropy and sharpened. Note that output map files from phenix.autosol and phenix.autobuild are still sharpened and corrected for anisotropy. - For MIR, if quick=True then as soon as a good solution is found with HySS all other derivatives are solved by difference Fouriers. This can speed up MIR structure solution. You can disable this feature with skip_hyss_other_derivs_if_quick=False. - AutoSol and AutoBuild: - It is now possible to specify a different number of copies of different chains in the sequence file. If the sequence file has n copies of chain A and m of chain B, it is now assumed that the stoichiometry is ncs_copies * (nA, mB). Previously it had been assumed always that the stoichiometry was ncs_copies *(A, B). - For structure determination with extremely little phase information there is a new keyword extreme_dm=True (default is False). This allows density modification to use parameters optimized for very poor phasing if the FOM of phasing is less than fom_for_extreme_dm. - AutoBuild - phenix.autobuild now requires that if a hires (or refinement) file is supplied, it must have a complete set of free R flags (test set) if the datafile also has a test set. In this case the test set from the datafile is ignored and the one from the hires/refinement file is used. - You can use the Phenix GUI to extend the test set from your datafile to match the data in your hires/refinement file if necessary. Molecular Replacement: ====================== - Phaser: - various speed enhancements - new normal modes analysis features for domain finding (phaser.splitter) - bug fixes - MR-Rosetta: - You can now tell mr_rosetta to ignore long-running sub-processes and just go on with the finished jobs. New commands: ============= - phenix.dynamics (new command): - simple Cartesian dynamics, replaces equivalent function in PDBTools - phenix.parallel_autobuild (new command): - a tool for running phenix.autobuild many times in parallel, picking the best results, and iterating with the new maps as a starting point. - can make effective use of as many as 40 processors. Ligands: ======== - phenix.ligand_pipeline: - numerous bug fixes - more flexible handling of input sequence files - optional Sculptor step prior to MR to fix residue identities - sidechain pruning enabled by default - interactive mode now includes ligand selection - phenix.guided_ligand_replacement: - Guided Ligand Replacement (GLR) can now search for a protein-ligand complex suitable for the guided fitting using web services on the PDB website or in a local directory. - GLR ligand input has been reworked to allow the use of the three-letter code relying on eLBOW to generate the restraints. - REEL: - simplification and improvement of molecule building - support for cis/trans E/Z enantiomers - view .geo files Miscellaneous: ============== - PDBTools: - simple dynamics option moved to new command, phenix.dynamics - remove_alt_confs and truncate_to_poly_ala options made compatible with other model modifications - HySS: - converted to use standard Phenix parameter syntax - Many new optional features: - Parallel pre-scoring of 2-site solutions - Parallel completion and scoring - Comparison with a fixed solution - Resolution cutoff for Phaser rescoring - Top-scoring solution written even if no matches found - All solutions written - Skip direct methods completion - LLG completion sigma cutoff - Scoring of input sites - Randomization of input sites 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 64, Room 248 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 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ LBenvenue(a)lbl.gov ][ 1-510-495-2506 ] --

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bad density for part of the electron density map
by Wei Shi 08 Oct '13

08 Oct '13

Hi all, I am working with a dataset in space P212121, resolution 2.8 amstrong, total completeness of the data 96.2% (98.1%), I/sigma 5.2 (3.1). This is a structure of a transcriptional factor (dimer) with the ligand. Upon ligand binding, there is conformational change in some part of the protein and I used the apo protein structure as a search model, and get a molecular replacement solution. After some rounds of refinement and rebuild (mainly in a region in the C-terminal ligand binding domain), the best refinement I have is as follows. But the electron density map for the C-terminal DNA binding (about 80 residues) is still very bad.... I tried to mutate them to alanine and do refinement and also tried to delete the whole region to do refinement, but both of the strategies didn't give me better density which I could use to rebuild the residues manually. I am wondering whether any of you have any ideas about what might go wrong and any suggestions about what to check or try next. Thank you so much! start final --------------------------------------- R-work: 0.3220 0.3100 R-free: 0.3916 0.3884 RMS(angles): 2.50 1.39 RMS(bonds): 0.016 0.010 Ramachandran outliers: 1.8% (Goal: < 0.2%) Ramachandran favored: 89.0% (Goal: > 98%) Rotamer outliers: 5.4% (Goal: 1%) C-beta outliers: 0 (Goal: 0) Clashscore: 11.50 Overall score: 2.71 Best, Wei

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Re: [phenixbb] metal coordination restrain on alternative conformation
by Zhang yu 07 Oct '13

07 Oct '13

Hi Nigel, Another question. How do I let phenix.refine know that all atoms in my ligand should have the same occupancy for one conformation? The occupancy refinement in phenix.refine assigned different occupancies to atoms in one conformation. Thanks Yu On Tue, Oct 1, 2013 at 6:10 PM, Zhang yu <phenixzyfish(a)gmail.com> wrote: > Thanks > > > On Tue, Oct 1, 2013 at 1:54 PM, Nigel Moriarty <nwmoriarty(a)lbl.gov> wrote: > >> I ran >> >> phenix.metal_coordination >> >> and got the attached. Pass it to phenix.refine. >> >> >> On Mon, Sep 30, 2013 at 6:53 PM, Zhang yu <phenixzyfish(a)gmail.com> wrote: >> >>> Hi Nigel, >>> >>> Thanks. Please see attached PDB file. The structure has two molecules in >>> one ASU. Each of molecule contains 6 protein chains and three Nucleic-acid >>> chains (i.e. chain A, B, C, D, E, F, G, H and I for molecule 1; chain K, L, >>> M, N, O, P, Q, R, and S for molecule 2) >>> >>> There is only one nucleoside-triphosphate and its cognate MG++ in each >>> molecule having alternative conformations (named as conformation A and B). >>> The desired restrains are as follows, >>> >>> In molecule 1, >>> atom_selection_1 = name MG,B and chain N and resname MG and resseq 2004 >>> atom_selection_2 = name OD2 and chain N and resname ASP and resseq 739 >>> distance_ideal = 2.090000 >>> >>> atom_selection_1 = name MG,B and chain N and resname MG and resseq 2004 >>> atom_selection_2 = name O3G, B and chain S and resname CMP and resseq >>> 2001 >>> distance_ideal = 2.090000 >>> >>> atom_selection_1 = name MG,B and chain N and resname MG and resseq 2004 >>> atom_selection_2 = name O1B,B and chain S and resname CMP and resseq >>> 2001 >>> distance_ideal = 2.090000 >>> >>> atom_selection_1 = name MG,A and chain N and resname MG and resseq 2004 >>> atom_selection_2 = name O1B,A and chain S and resname CMP and resseq >>> 2001 >>> distance_ideal = 2.090000 >>> >>> atom_selection_1 = name MG,A and chain N and resname MG and resseq 2004 >>> atom_selection_2 = name O1G,A and chain S and resname CMP and resseq >>> 2001 >>> distance_ideal = 2.090000 >>> >>> In molecule 2, >>> atom_selection_1 = name MG,B and chain D and resname MG and resseq 2004 >>> atom_selection_2 = name OD2 and chain D and resname ASP and resseq 739 >>> distance_ideal = 2.090000 >>> >>> atom_selection_1 = name MG,B and chain D and resname MG and resseq 2004 >>> atom_selection_2 = name O3G, B and chain I and resname CMP and resseq >>> 2001 >>> distance_ideal = 2.090000 >>> >>> atom_selection_1 = name MG,B and chain D and resname MG and resseq 2004 >>> atom_selection_2 = name O1B,B and chain I and resname CMP and resseq >>> 2001 >>> distance_ideal = 2.090000 >>> >>> atom_selection_1 = name MG,A and chain D and resname MG and resseq 2004 >>> atom_selection_2 = name O1B,A and chain I and resname CMP and resseq >>> 2001 >>> distance_ideal = 2.090000 >>> >>> atom_selection_1 = name MG,A and chain D and resname MG and resseq 2004 >>> atom_selection_2 = name O1G,A and chain I and resname CMP and resseq >>> 2001 >>> distance_ideal = 2.090000 >>> >>> >>> >>> >>> >>> On Mon, Sep 30, 2013 at 6:31 PM, Nigel Moriarty <nwmoriarty(a)lbl.gov>wrote: >>> >>>> Can you send the residues involved? >>>> >>>> Nigel >>>> >>>> NB. Any files sent to me will be held in strictest confidence. >>>> >>>> >>>> >>>> On Mon, Sep 30, 2013 at 12:51 PM, Zhang yu <phenixzyfish(a)gmail.com>wrote: >>>> >>>>> Hi everyone, >>>>> >>>>> My structure contains a metal coordinating to some residues, one of >>>>> which has alternative conformations. Phenix doesn't pickup the residue with >>>>> alternative conformation when I tried to generate metal restrains using >>>>> ready.set. >>>>> >>>>> Any idea? Thanks >>>>> >>>>> Yu >>>>> >>>>> _______________________________________________ >>>>> phenixbb mailing list >>>>> phenixbb(a)phenix-online.org >>>>> http://phenix-online.org/mailman/listinfo/phenixbb >>>>> >>>>> >>>> >>>> >>>> -- >>>> Nigel W. Moriarty >>>> 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 >>>> >>>> _______________________________________________ >>>> phenixbb mailing list >>>> phenixbb(a)phenix-online.org >>>> http://phenix-online.org/mailman/listinfo/phenixbb >>>> >>>> >>> >> >> >> -- >> Nigel W. Moriarty >> 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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Refinement going wild in latest versions
by Hugues Nury 04 Oct '13

04 Oct '13

Hello everyone, I am experiencing differences with phenix.refine versions 1.8.3 or 1.8.4 compared to 1.8.2. Performing comparable runs, Rs are rising several percents with the latest versions, while marginally decreasing using version 1.8.2. I am a very recent convert to Phenix, so maybe I'm missing something obvious, but here are the details: Refinement strategy is xyz+real space+tls+individual Bs at 3.5 A, using NCS and secondary structure restraints, and weight optimization. Starting R/Rfree are around 24.5/28.5 Part of the problem seems to come from secondary structure restraints, with (many) messages in the log file of the refinement going wild looking like WARNING: could not process nonbonded pair Original error: cctbx Internal Error: /net/clover/scratch1/phenix/phenix-1.8.4-1496/cctbx_project/cctbx/crystal/pair_tables.h(663): CCTBX_ASSERT(j_sym >= 0) failure. pdb=" N GLN B 130 " segid="B " pdb=" O VAL B 115 " segid="B " In log files of refinement with version 1.8.2, there are no such messages, and in either case the definition of beta strands were done automatically by Phenix But even secondary structure restraints are switched off, it starts ok but goes wrong at the beginning of cycle 2, during local real space refinement start: r_work=0.2271 r_free=0.2785 final: r_work=0.2418 r_free=0.2937 And then continue to worsen. Any help appreciated! Cheers, Hugues -- Hugues Nury Institut de Biologie Structurale 41 rue Jules Horowitz, F-38027 Grenoble Cedex 1, France +33 6 52 45 17 79

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REMARK 3 NCS
by Luca Pellegrini 03 Oct '13

03 Oct '13

Hello, I have noticed that Phenix 1.8.4-1496 (as well as 1.8.3-1479) appears to have stopped writing the REMARK 3 NCS in the PDB header. Is this so? It is useful to have that info when it comes to depositing the coordinates. Many thanks, Luca Luca Pellegrini Department of Biochemistry University of Cambridge 80 Tennis Court Road Cambridge CB2 1GA - UK Email: lp212(a)cam.ac.uk Tel: 0044-1223-760469 Fax: 0044-1223-766002 Sanger building, room 3.59

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DEN refinement
by Jan van Agthoven 02 Oct '13

02 Oct '13

Hi everyone, I ran a DEN refinement of my low resolution structure (3.6) to improve my model. I typed in the following command: phenix.den_refine model.pdb data.mtz den.reference_file=reference.pdb reference.params with reference.params saying: refinement.reference_model.reference_group { reference = chain A and resseq 1:953 selection = chain A and resseq 1:953 } refinement.reference_model.reference_group { reference = chain B and resseq 1:687 selection = chain B and resseq 1:687 } because the reference file only contains chain A and chain B. Unfortunately I obtained much worse R factors then with a regular refinement: Start R-work = 0.2798, R-free = 0.3176 Final R-work = 0.3733, R-free = 0.4089 Does someone have an idea what could have go wrong? Thanks,

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phaser error
by Alexander Batyuk 02 Oct '13

02 Oct '13

Dear developers, I'm getting the following error while running phaser: ERROR running main function (UNHANDLED): cctbx Error: Lattice type not specified. It comes when I put one placed model (found in a previous run) and search for another. Phenix version 1.8.4, on OSX 10.8.5 Do you have any suggestions? Best wishes, Alex -- Alex Batyuk The Plueckthun Lab www.bioc.uzh.ch/plueckthun

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MR-SAD in phenix
by LISA 01 Oct '13

01 Oct '13

Hi All, If we have partial model we can run MR_SAD by adding a single new keyword to my AutoSol run: input_partpdb_file=MR.pdb But I only have a mtz file not a pdb file in the molecular replacement result with EM map as the model. How can I combine the EM result with SAD to improve the density? I have Ta6Br12 cluster soaked crystal data. How can I define the cluster? How much of F'' and F' of this cluster at the wavelength of 1.254A? Thank you. Lisa

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Plotting disabled
by Luca Pellegrini 01 Oct '13

01 Oct '13

Hello, Phenix.refine (1.8.4-1496) disables plotting in the GUI, complaining that the libpng15.15.dylib is missing (see screen below). The library is actually there, where Phenix says it should be: /opt/X11/lib/libpng15.15.dylib. How do I get Phenix to load it? I am using Mac OSX 10.6.8. Many thanks, Luca Luca Pellegrini Department of Biochemistry University of Cambridge 80 Tennis Court Road Cambridge CB2 1GA - UK Email: lp212(a)cam.ac.uk Tel: 0044-1223-760469 Fax: 0044-1223-766002 Sanger building, room 3.59

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