[phenixbb] Phenix version 1.12 released

Paul Adams pdadams at lbl.gov
Fri Jul 14 09:36:51 PDT 2017

The Phenix developers are pleased to announce that version 1.12 of Phenix is now available (build 1.12-2829). Binary installers for Linux, Mac OSX, and Windows platforms are available at the download site:


Highlights for this version:

New tools for secondary structure validation, comparing multiple related structures, cryo-EM model and map validation, and calculation of real space difference maps. Video tutorials are now available on the new Phenix Tutorial YouTube channel (www.youtube.com/c/phenixtutorials). A suite of tools for cryo-EM model building and structure refinement including automated map sharpening, segmentation, and model building. Real space refinement now has an option to use histogram equalized map as a refinement target. Phaser version 2.8 has several new features, including unit cell refinement for EM data, more extensive use of eLLG in decision making and analysis, anomalous substructure determination (Phassade), improved tNCS detection and analysis, and improvements to SCEDS. 


  - phenix.secondary_structure_validation - tool to validate secondary structure
    section in .pdb and .mmcif files with option to filter bad annotations.

  - Structure Comparison: tool for parallel validation and analysis of
    near-identical protein structures. Results include the analysis of ligands,
    rotamers, Ramachandran angles, missing atoms, water locations and B-factors.

  - phenix.mtriage: command-line tool to validate cryo-EM models. GUI is
    available. Computes various map statistics including resolution estimates,
    FSC between half-maps, full and model maps. Outputs mask file used to
    compute FSC. Still under development.

  - phenix.real_space_diff_map: command-line tool to compute difference map.
    This is a real-space analogue of Fo-Fc map mainly designed for cryo-EM maps.
    See http://phenix-online.org/newsletter/CCN_2017_01.pdf for details.


  Video tutorials about Phenix tools are now available on the Phenix Tutorial
  YouTube channel (www.youtube.com/c/phenixtutorials).

  The following topics are covered:
  - How to run phenix.refine
  - How to calculate polder maps
  - How to run phenix.real_space_refine
  - How to run PDB tools
  - How to change phenix.refine parameters via the GUI
  - Basic Phenix eLBOW tutorial
  - How to run Phaser-MR from the Phenix GUI
  - Explaining the atom selection syntax
  - How to run Structure Comparison


  - Phenix.auto_sharpen:  New map sharpening algorithms available based on
      (1) optimization of map clarity (adjusted surface area or kurtosis),
      (2) resolution-dependent map-model correlation,
      (3) resolution-dependent half-map correlation, and
      (4) local map sharpening

  - Phenix.map_to_model: Iterative map improvement using model from one
      cycle to optimize sharpening of the map for the next cycle

  - Phenix.map_to_object:  Now you can individually map each member of a
     group of chains onto your target

  - Phenix.chain_comparison: Now can compare a target to each of a group of

  - Phenix.find_alt_orig_sym_mate: Now uses ssmalignment.stats to see what
    residue pairs were included by ssm in a hypothetical calculation of
    the ssm-rmsd. This is to avoid including atoms that even for an optimal
    structural alignmentwould have been too far apart that ssm would use them.
    Excluding these is necessary to avoid having the calculated rmsd blow up.

  - Now using angles for restraining hydrogen bonds in alpha helices and
    beta sheets in secondary structure restraints.

  - Phenix.polder: New option (compute_box=True) to compute a difference map
    excluding the bulk solvent mask within a user-defined box. The map can be
    used to inspect interesting difference density peaks.

  - phenix.map_model_cc (phenix.model_map_cc): various enhancements and bug

  - phenix.real_space_refine:
    - improved ADP refinement (still group)
    - improved NCS constraints definition
    - multi-model PDB file is not output by default anymore
    - (experimental) option to use masked histogram equalized map as refinement
      target. Using such map dramatically improves refined model geometry. This
      map is not suitable for ADP refinement.
    - show CCmask, CCvolume and CCpeaks that report on local and gloabal model
      to map fit.


  - Specialised restraints for ligands with differing chemistry in the same
    model allows using the same 3-letter code but different restraints for
    a specific instance - apply_cif_restraints

  - Detailed control of peptide planes and omega angles
    - apply_all_trans
    - apply_peptide_plane
    - apply_cis_trans_specification: use an atom selection (CA) to force a
      cis or trans omega angle

  - Improvements to robustness and features

  - New interfaces
    - phenix.mtriage
    - phenix.map_box
    - phenix.auto_sharpen
    - phenix.map_to_model
    - phenix.ncs_average (under "Other Tools")
    - phenix.sculpt_ensemble (alpha)
  - Updated interfaces
    - Comprehensive Validation shows real-space correlations from
      phenix.map_model_cc when map files are used
    - Structure Comparison

- Validation
  - improved speed of clashscore validation
  - bug fix to handling of cis-peptides in ramalyze
  - contours for ramalyze, rotalyze, and cablam now accessible at
  - validation GUI now shows altloc identifirs for most outliers
  - improved internal code accessibility of validation statistics

- Phaser-2.8.0

  - refinement of cell for data (electron micrcoscopy)
  - more analysis using eLLG for component addition 
  - more analysis using eLLG for polyalanine residues for target eLLG given rms
  - more analysis using eLLG for single atoms more ordered than average
  - more analysis using eLLG for chains/gyre-and-gimble
  * Phassade: Fast Fourier Transform Anomalous Substructure Determination
  - SOLU TRIAL records RF-LLG for trial orientation
  - gyre and translation function report RF recorded for trial orientations 
  - 'scons --ccp4' command line flag for ccp4 build (generates ccp4-style headers)
  * improved tNCS detection and analysis
  * gyre and gimble improved for output and python scripting
  * NMA outputs all perturbed files in MODEL delimited pdb file '<fileroot>.nma.pdb'
  * sceds outputs domains to chain delimited file '<fileroot>.nma.pdb'
  - sceds domain pdb file have TER separated domains
  - NMA option to output separate pdb files for each perturbation (XYZOUT NMA ALL OFF)
  - sceds option to output separate pdb files for each domain (XYZOUT NMA ALL OFF)
  - NMA has option to turn off output of input coordinates (NMA ORIG ON)
  - pdb chain identifies can be left unchanged from input (XYZOUT CHAIN COPY) (for Eleanor)
  - bugfixes
  --  allow peaks and purge percent to override one another if not default
  --  rms estimation developer options not being set correctly
  --  throw out of memory error if Patterson map allocation fails

For a full list of changes see:


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:


There is a Phenix bulletin board:


Please consult the installer README file or online documentation for
installation instructions.

Direct questions and problem reports to the bulletin board or:

	help at phenix-online.org and bugs at 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
Division Director, Molecular Biophysics & Integrated Bioimaging, 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

Lawrence Berkeley Laboratory
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Berkeley, CA 94720, USA.

Executive Assistant: Louise Benvenue [ LBenvenue at lbl.gov ][ 1-510-495-2506 ]

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