- phenixbb - phenix-online.org

Phenix version 1.6.4 released
by Paul Adams 31 Jul '10

31 Jul '10

The Phenix developers are pleased to announce that version 1.6.4 of Phenix is now available. Binary installers for Linux, and Mac OSX platforms are available at the download site: http://phenix-online.org/download/ Just some of the new features in this version (1.6.4) are: - GUI: - new interfaces for eLBOW, CIF to MTZ conversion, phenix.find_ncs, phenix.superpose_maps - new structure comparison tool (evaluation of multiple related structures) - supports execution of jobs on the Sun Grid Engine queueing system - maps for PyMOL now output in (smaller, faster) CCP4 format - display of sequence and secondary structure in wizards and validation - new wide-format windows for wizards and phenix.refine - many bug fixes - Automated model building: - phenix.autosol now much faster and improved model-building after density modification - phenix.phase_and_build (carries out an iterative process of building a model as rapidly as possible and uses this model in density modification to improve the map. Up to 10x faster compared to AutoBuild, but model quality is nearly as good) - phenix.build_one_model (quickly build a single model from a map and sequence file, or extend an existing model) - phenix.assign_sequence (carry out an improved sequence assignment of a model that you have already built. Uses the new loop libraries available in phenix.fit_loops) - phenix.apply_ncs (apply NCS operators to a single copy of a protein to create all the NCS‐related copies) - phenix.find_ncs (now supports identification of NCS operators from a density map) - phenix.fit_loops (two main algorithms now available - fit short gaps using a loop library derived from high‐resolution structures in the PDB, or build loops directly by iterative extension with tripeptides - phenix.refine: - reference model restraints (restraint dihedral angles to a higher resolution reference model) - alternate ideal angles for torsion definitions (preserves side chain rotameric states) - automatic flipping of incorrect N/Q/H rotamers - custom planarity restraints - hydrogen-bond restraints for Watson-Crick base pairs - reflections with Fobs=0 used in refinement - automatic optimization of mask parameters - map parameters now consistent with phenix.maps - new custom_nonbonded_symmetry_exclusions atom selection parameter to fine tune non-bonded interactions across symmetry axes - Phasing: - Option for Phaser likelihood scoring of substructure solutions in HySS - SOLVE converted to C++; FORTRAN compiler no longer required for Phenix compilation - Other: - KiNG kinemage viewer incorporated into Phenix - Real space refinement option in ligand fitting - B-factor sharpening option for maps For a full list of changes see: http://www.phenix-online.org/documentation/CHANGES Please note that there is a new publication that 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 Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Head, Berkeley Center for Structural Biology Building 64, Room 248 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: Marian Harris [ MSHarris(a)lbl.gov ] [ 1-510-486-6886 ] --

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what should I do after making an iterative-build omit map
by J J 30 Jul '10

30 Jul '10

Hello everyone, I used default setting in phenix and made an iterative-build omit map (it took 3 days!!!). Input: a pdb file (6 identical chains in AU); an mtz file output: a resolve_composite_map.mtz; an overall_best_edited.pdb questions: 1) There is only one chain in overall_best_edited.pdb, the resolve_composite_map.mtz clearly indicates there are 6 chains in AU. 2) What's the next step for me after obtaining resolve_composite_map.mtz? a) use phenix.refine to do refinement? if this is the case, what files should I use? b) use phenix.assign_sequence to assign sequence to resolve_composite_map.mtz? c) something else? Thanks in advance. Jason U Pitt

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r_free_flags.generate
by wtempel 30 Jul '10

30 Jul '10

Dear colleagues, I would like to confirm which, if any, twin laws/symmetry operators were applied during a given run of "r_free_flags.generate", but I cannot find the information in the log file of phenix.refine. Am I missing something? If not, could the program be modified to write out that information? In my concrete example, I ran phenix refine with a scalepack file in P4, for which xtriage suggested a P422 point group. Thank you, Wolfram Tempel

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Five sets of PDFs about Refinement, Maps, Validation and PHENIX
by Pavel Afonine 29 Jul '10

29 Jul '10

Hi Everyone, recently I had to update or do from scratch my talk "slides" on various subjects such as crystallographic structure refinement, maps, validation and some general PHENIX overview. Since I spent pretty significant amount of time making all these "slides" , ... I was thinking that may be this might be of use for some of you, so here it is... - 42 pages of general introduction to structure refinement: http://www.phenix-online.org/presentations/latest/pavel_refinement_general.… - 45 pages of phenix.refine overview (including extended details about its use from the command line): http://www.phenix-online.org/presentations/latest/pavel_phenix_refine.pdf - 42 pages of "Some Facts About Maps": http://www.phenix-online.org/presentations/latest/pavel_maps.pdf - 50 pages of "Crystallographic Structure Validation": http://www.phenix-online.org/presentations/latest/pavel_validation.pdf - 31 pages of introduction to PHENIX: http://www.phenix-online.org/presentations/latest/pavel_phenix_intro.pdf Most of the slides in "Introduction to PHENIX" came from Paul Adams, Tom Terwilliger and Nat Echols. Thanks Nat and Jeff Headd for providing with interesting examples of structures with unusual geometry. All the best! Pavel.

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Fwd: autobuild failure
by abhishek dey 29 Jul '10

29 Jul '10

---------- Forwarded message ---------- From: abhishek dey <41.abhishek(a)gmail.com> Date: 29 July 2010 21:27 Subject: autobuild failure To: phenixbb(a)phenix-online.org Dear all, I am facing some problem while running the Autobuild option for PHENIX-1.6-289 version. I uploaded the mtz file, sequence of my protein and the pdb file and started running AUTOBUILD. but the program stopped with the following error message SG: P 2 21 21 Cell: [49.539999999999999, 99.140000000000001, 144.41999999999999, 90.0, 90.0, 90.0] Inverse hand of space group: P 2 21 21 Creating sg entry from /data/dey/2779/rv2779p22121_sort2.mtz Unit cell: (49.54, 99.14, 144.42, 90, 90, 90) Space group: P 2 21 21 (No. 18) Space group name is: P 2 21 21 symbol is: p22121 **************************************** AutoBuild Input failed Need a symfile for solve .the working spacegroup is P 2 21 21 it will be helpful if someone give useful suggestion on this. thanks in advance -- Abhishek Dey

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Re: [phenixbb] phenixbb Digest, Vol 56, Issue 30
by Leonid Flaks 29 Jul '10

29 Jul '10

> Message: 4 > Date: Tue, 27 Jul 2010 08:39:17 -0700 > From: Nathaniel Echols<nechols(a)lbl.gov> > To: PHENIX user mailing list<phenixbb(a)phenix-online.org> > Subject: Re: [phenixbb] 32-bit binaries for version 1.6.3-473 > Message-ID: > <AANLkTinSzHiX4z9VPsrbMLFY7xFuwqwkghzCzj2WPjmd(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > On Tue, Jul 27, 2010 at 8:15 AM, Leonid Flaks<flaks(a)bnl.gov> wrote: > > >> I am running phenix 1.6.2-432 on a set of systems running 32-bit version of >> fedora-12. The latest version of phenix (1.6.3-473) has binaries mostly for >> 64-bit OS. The only 32-bit OS I see is fedora-3. I would be happy to switch >> to 64-bit OS one day, but HKL2000 that runs on the same computers has a big >> warning about instability of it on the 64-bit (it is dated back to 2005!) >> Coot is also crashing on the the 64-bit test system, so I have to stay with >> 32-bit for now. >> Does anybody know if fc-3 version would run on f-12? >> >> > I suspect it will be okay, but I haven't tested it. It partly depends on > which features will be used - the GUI is twitchier about system libraries on > Linux. Fortunately, we also distribute all of the source code for Phenix, > so if the binary installer doesn't work, I'd recommend switching to the > source installer. Are these the same machines (and OS) that were used for > RapiData? > > Yes, same 'cafe' systems. They all run f-12-32bit. > Would it be possible to have 32-bit version built for f-12 or f-13? > >> > Possibly - we are probably going to pull some machines from our queueing > system because they have only 8 cores, and some of these will become build > machines for additional platforms (64-bit Ubuntu and CentOS are candidates). > Also, we now build a CentOS 5 (similar to FC6) installer - it didn't work > properly for 1.6.3, but I think I've fixed it now, and we're going to push > out a 1.6.4 very soon because of some unrelated problems in 1.6.3. > > -Nat > > And on top of that, I don't see coot with python binary available for f-12 anymore. I will be testing fc-3 version then. Leon

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32-bit binaries for version 1.6.3-473
by Leonid Flaks 27 Jul '10

27 Jul '10

Hi! I am running phenix 1.6.2-432 on a set of systems running 32-bit version of fedora-12. The latest version of phenix (1.6.3-473) has binaries mostly for 64-bit OS. The only 32-bit OS I see is fedora-3. I would be happy to switch to 64-bit OS one day, but HKL2000 that runs on the same computers has a big warning about instability of it on the 64-bit (it is dated back to 2005!) Coot is also crashing on the the 64-bit test system, so I have to stay with 32-bit for now. Does anybody know if fc-3 version would run on f-12? Would it be possible to have 32-bit version built for f-12 or f-13? Thanks, Leon

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LigandFit parameters?
by Hermella Woldemdihin 27 Jul '10

27 Jul '10

Hi, I am using LigandFit on the GUI version of Phenix. In my electron density map there is a good density for my ligand. And I have my ligand in pdb format. As an input to LigandFit I gave my ligand file(pdb), an MTZ file from my data processing and my protein at some stage of refinement (@ a good R-values). I used the default settings (Resolution=0, Minimum CC of ligand to map=0.75 and Ligand map shape=Fo-Fc) and I got a bad result. My overall CC=0.33 and Score=68.68). What shall I do to get the best solution??? Thanks all! Hermi

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Planarity restraint for covalent linkage
by Elwood A. Mullins 24 Jul '10

24 Jul '10

I'm trying to refine a thioester linkage (CoA to glutamate). Is it possible to define planarity restraints in a refinement.geometry_restraints.edits file along with bonds and angles? If not, what would be the best way to restrain the linkage?

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questions about ncs copy in autobuild
by J J 23 Jul '10

23 Jul '10

Dear All, I am using phenix.autobuild .eff file to build a structure (version 1.6.1). For the input I have a pdb model file with 6 chains; a sequence file which contains residues of a single chain (the sequence file has a few more residues at N-terminal than the pdb model file); an mtz amplitude file; I also specified ncs_copies=6 (I know there are 6 copies in the au). What confuses me is the output pdb file only has one chain (huge Rwork&Rfree, >0.5). Should there be 6 chains? The other issue is that the output chain has fewer residues than my sequence file (both N&C-terminal). It also has fewer residues compared with the pdb model file. Is this because I do not have enough resolution to resolve those missing residues? Thanks in advance. Jason U Pitt

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