[phenixbb] Phenix version 1.10 released

Paul Adams pdadams at lbl.gov
Tue Sep 8 10:37:03 PDT 2015

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:


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. 

- 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
  - 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

- 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

- phenix.structural_domain_search:
  - Domain search program using an approach based on graph theory. Very quick and
    fairly accurate for simple problems.

- 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):

- 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
  - current version obsoletes all previous versions

- phenix.chains_as_models:
  Convert PDB file with multiple chains into PDB file with multiple models

- 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:


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
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
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Tel: 1-510-486-4225, Fax: 1-510-486-5909

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

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