Phaser Crystallographic Software

From Phaserwiki

Phaser is a program for phasing macromolecular crystal structures with maximum likelihood methods. It has been developed by Randy Read's group at the Cambridge Institute for Medical Research (CIMR) in the University of Cambridge and is available through the Phenix and CCP4 software suites.

Use the sidebar to navigate through the extensive documentation for Phaser.

This PhaserWiki supersedes the obsolete Phaser homepage, which now redirects to this wiki. A copy of the obsolete Phaser homepage can be found here

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Currently Supported Releases


Download with Phenix Nightly Builds → Phenix
Documentation → Manual


Download with Phenix Nightly Builds → Phenix
Download with CCP4 Update 7.0.023
Documentation → Manual

Changelog highlights

  • add feature to filter out data with low information content particularly in cases of high anisotropy
  • bugfixes
solution history formatting
R-value test with multiple search components failing
limit number of permutations in amalgamation to stop combinatorial explosion
correct handling of effect of experimental error in fast rotation function
search method full & permutations on had corrupted search ensemble copy numbers


Download with Phenix Official Release 1.11.1 (October 2016) → Phenix
Documentation → Manual

Changelog highlights

  • SOLUTION HISTORY tracks solution through positions in RF/TF/PAK/RNP peak lists
  • selection by CHAIN and MODEL for PDB coordinate entry
  • ensemble member rmsds adjusted to give values consistent with rmsd between members of an ensemble
  • automatic search number for search ensemble(s)
  • packing trace can be entered independently of coordinates and map (can mask larger volume than model)
  • read TNCS/anisotropy binary files to avoid refinement (non-python interface)
  • write TNCS and anisotropy parameters to binary files (non-python interface)
  • default reading of I (or failing that, F) from mtz file (LABIN optional)
  • trace for ensembles from maps = hexgrid of 1000+/-100 points
  • trace for ensembles from coordinates above 1000 C-alpha = hexgrid of 1000+/-100 points
  • trace for ensembles from coordinates between 1000 atoms and 1000 C-alpha = Calpha atoms
  • trace for ensembles from coordinates under 1000 atoms = all atoms
  • packing by pairwise percent only, other packing modes obsoleted
  • packing test during FTF run by default with 50% pairwise packing cutoff
  • automatic tNCS NMOL determination in presence of commensurate modulation
  • added MODE GIMBLE, which splits ensembles by chain for rigid body refinement
  • support for unicode
  • solution coordinates placed nearest to input coordinates if possible

Referencing Phaser

Citing crystallographic software in your paper is important for funding new software development. We rely on your citations to convince funding bodies that our software is being used.

If you solve a structure with Phaser, please cite

Phaser crystallographic software
McCoy AJ, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC, Read RJ.
J Appl Cryst (2007). 40, 658-674.