- phenixbb - phenix-online.org

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

3 3

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

3 3

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,

2 2

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

1 0

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

2 1

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

2 1

metal coordination restrain on alternative conformation
by Zhang yu 30 Sep '13

30 Sep '13

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

2 1

DEN refinement stuck
by Jan van Agthoven 24 Sep '13

24 Sep '13

Hi, I launched a DEN refinement 4 hours ago, and it remain stuck with the following message: ----------coordinate minimization before annealing---------- Running DEN torsion optimization on 1 processors... Running torsion simulated annealing ...trying gamma 0.0, weight 3.0 Is this normal? Is torsion simulated annealing so long? Thanks,

2 2

Merging two or more dataset
by Singh, Bishal 24 Sep '13

24 Sep '13

Is it possible to merge two or more dataset of same protein of different crystals? If yes, please suggest me the way. I shall be grateful for your help. Bishal Singh PhD student University of Heidelberg, Germany

2 1

Workshop on the PDBx/mmCIF Data Exchange Format For Structural Biology (October 22, 2013) and PSI Workshop on Theoretical Model Archiving and Validation (October 21, 2013)
by Torsten Schwede 24 Sep '13

24 Sep '13

*Workshop on the PDBx/mmCIF Data Exchange Format For Structural Biology* Center For Integrative Proteomics Research Rutgers, The State University of New Jersey Tuesday October 22, 2013 http://www.proteinmodelportal.org/workshop-2013/ The wwPDB has established PDBx/mmCIF as the new standard format for data exchange and archiving in structural biology (http://www.wwpdb.org/news/news_2013.html#22-May-2013). To help facilitate the transition from PDB to PDBx/mmCIF format the wwPDB is organizing a programmer's workshop describing the content and organization of PDBx/mmCIF data, and the available software tools and libraries supporting PDBx/mmCIF (C/C++, Java, and Python). The workshop will be held on Tuesday, October 22, 2013 at Rutgers, The State University of New Jersey (in conjunction with a PSI Workshop on Theoretical Model Archiving and Validation to be held Monday, October 21, 2013): Starting at 9am, the morning session will include presentations from: Paul Adams (Phenix), David Case (AMBER), Tom Goddard (UCSF Chimera), Robert Hanson (JMol), Eugene Krissinel (CCP4/mmdb), Andreas Prilic (BioJava), John Westbrook (RCSB PDB). The afternoon session will offer an opportunity to work hands-on with the presenters and developers in the areas of structural biology and molecular modeling to learn application details and to discuss successful approaches and experiences in adapting software to support PDBx/mmCIF. In addition, the workshop will include a discussion of PDBx/mmCIF extensions required to represent molecular modeling specific information. There is no registration fee, but online registration is required (registration Deadline is October 4). For detailed agenda and online registration: http://www.proteinmodelportal.org/workshop-2013/ Looking forward to welcoming you at the workshop, Andrej Sali, John Westbrook, and Torsten Schwede ---- Prof. Dr. Torsten Schwede Biozentrum Universität Basel & SIB Swiss Institute of Bioinformatics Klingelbergstrasse 50-70 4056 Basel

1 0