Modes

Phaser runs in different modes, which perform Phaser's different functionalities. Modes can either be basic modes or modes that combine the functionality of basic modes.

Phaser Executable

The Phaser executable runs in different modes, which perform Phaser's different functionalities. The mode is selected with the MODE keyword.

Python Interface

Phaser can be compiled as a python library. The mode is selected by calling the appropriate run-job. Input to the run-job is via input-objects, which are passed to the run-job. Setter function on the input objects are equivalent to the keywords for input to the phaser executable. See Python Interface for details.

Modes

Automated Molecular Replacement

MODE MR_AUTO

Combines cell content analysis, anisotropy correction, translational NCS analysis, fast rotation and translation functions, and refinement and phasing to automatically solve a structure by molecular replacement

 ResultMR r = runMR_AUTO(i=InputMR_AUTO)

Rotation Function

MODE MR_ROT

Combines the anisotropy correction, translational NCS analysis, and EITHER likelihood-enhanced fast rotation function, by default rescored with the full rotation likelihood function OR a brute-force search of angles using the full likelihood rotation function

 ResultMR_RF r = runMR_FRF(i=InputMR_FRF)

Translation Function

MODE MR_TRA

Combines the anisotropy correction, translational NCS analysis, and EITHER likelihood-enhanced fast translation function, by default rescored by the full likelihood translation function OR a brute force search of positions using the full likelihood translation function to find the position of a previously oriented model

 ResultMR_TF r = runMR_FTF(i=InputMR_FTF)

Packing

MODE MR_PAK

Determines whether molecular replacement solutions pack in the unit cell using a C-alpha clash test

 ResultMR r = runMR_PAK(i=InputMR_PAK)

Refinement and Phasing

MODE MR_RNP

Combines the anisotropy correction, translational NCS analysis, and refinement against the likelihood function to optimize full or partial molecular replacement solutions and phase the data. At the end of refinement, the list of solutions is checked for duplicates, which are pruned

 ResultMR r = runMR_RNP(i=InputMR_RNP)

Anisotropy Correction

MODE ANO

Corrects the experimental data (amplitude and associated sigma) for anisotropy. First, the anisotropy is removed by scaling up data from weak directions and scaling down data from strong directions, preserving the overall equivalent isotropic B-factor. Then (as suggested by Strong et al. (2006), PNAS 103:8060-8065), the data are resharpened to restore the original falloff in the strong direction. The amount of resharpening can be controlled with the RESHARP keyword.

 ResultANO r = runANO(i=InputANO)

Translational NCS and Twin analysis

MODE NCS

Finds pseudo-translational NCS vectors and corrects the data for intensity variations due to the ptNCS using likelihood methods. The data are corrected for anisotropy first and analysed for twinning before and after data correction.

 ResultNCS r = runNCS(i=InputNCS)

Cell Content Analysis

MODE CCA

Determines the composition of the crystals using the "new" Matthews coefficients of Kantardjieff & Rupp (2003) ("Matthews coefficient probabilities: Improved estimates for unit cell contents of proteins, DNA and protein-nucleic acid complex crystals". Protein Science 12:1865-1871). The molecular weight of ONE complex or assembly to be packed into the asymmetric unit is given and the possible Z values (number of copies of the complex or assembly) that will fit in the asymmetric unit and the relative frequency of their corresponding VM values is reported.

 ResultCCA r = runCCA(i=InputCCA)

Normal Mode Analysis

MODE NMA

Writes out pdb files that have been perturbed along normal modes, in a procedure similar to that described by Suhre & Sanejouand (Acta Cryst. D60, 796-799, 2004). Each run of the program writes out a matrix FILEROOT.mat that contains the eigenvectors and eigenvalues of the atomic Hessian, and can be read into subsequent runs of the same job, to speed up the analysis.

 ResultNMA r = runNMA(i=InputNMA)

Automated Experimental Phasing

MODE EP_AUTO

Combines anisotropy correction, translational NCS analysis, cell content analysis, and SAD phasing to automatically solve a structure by experimental phasing

 ResultEP r = runEP_AUTO(i=InputEP_AUTO)

Single Atom Molecular Replacement

MODE MR_ATOM

Combines automated molecular replacement with log-likelihood gradient completion to solve high resolution structures by single atom MR. The data are prepared with runMR_DAT and then the phasing is done withing the EP_AUTO mode.

 ResultEP r = runMR_ATOM(i=InputMR_ATOM)

Keywords Relevant to Each Mode

Mode	Relevant Keywords
MR_AUTO	BFACTOR BINS BOXSCALE CELL CLMN COMPOSITION DEBUG ELLG ENSEMBLE HKLIN HKLOUT JOBS KEYWORDS MACANO MACMR MACTNCS MUTE NORMALIZATION OUTLIER PACK PEAK PERMUTATIONS PTGROUP PURGE REFLECTIONS RESCORE RESHARPEN RESOLUTION RFACTOR ROOT ROTATE SAMPLING SEARCH SGALTERNATIVE SOLPARAMETERS SOLUTION SPACEGROUP TARGET TITLE TNCS TOPFILES TRANSLATE VERBOSE XYZOUT ZSCORE
MR_ROT	BINS BOXSCALE CELL CLMN COMPOSITION DEBUG ENSEMBLE JOBS KEYWORDS MACANO MACTNCS MUTE NORMALIZATION OUTLIER PEAKS PURGE REFLECTIONS RESCORE RESHARPEN RESOLUTION RFACTOR ROOT ROTATE SAMPLING SEARCH SGALTERNATIVE SOLPARAMETERS SOLUTION SPACEGROUP TARGET TITLE TNCS TOPFILES VERBOSE XYZOUT
MR_TRA	BINS BOXSCALE CELL COMPOSITION DEBUG ENSEMBLE HKLIN HKLOUT JOBS KEYWORDS MACANO MACTNCS MUTE NORMALIZATION OUTLIER PEAKS PTGROUP PURGE REFLECTIONS RESCORE RESHARPEN RESOLUTION RFACTOR ROOT SAMPLING SEARCH SGALTERNATIVE SOLPARAMETERS SOLUTION SPACEGROUP TARGET TITLE TNCS TOPFILES TRANLATE VERBOSE XYZOUT ZSCORE
MR_RNP	BFACTOR BINS BOXSCALE CELL COMPOSITION DEBUG ENSEMBLE HKLIN HKLOUT JOBS KEYWORDS MACANO MACMR MACTNCS MUTE NORMALIZATION OUTLIER PTGROUP REFLECTIONS RESHARPEN RESOLUTION ROOT SOLPARAMETERS SOLUTION SPACEGROUP TITLE TNCS TOPFILES VERBOSE XYZOUT
MR_PAK	CELL DEBUG ENSEMBLE JOBS KEYWORDS MUTE PACK PTGROUP ROOT SOLUTION SPACEGROUP TITLE TOPFILES VERBOSE XYZOUT ZSCORE
ANO	BINS CELL COMPOSITION DEBUG HKLNI HKLOUT MACANO MUTE NORMALIZATION REFLECTIONS RESHARPEN RESOLUTION ROOT SPACEGROUP TITLE VERBOSE
CCA	CELL COMPOSITION DEBUG MUTE RESOLUTION ROOT SPACEGROUP TITLE VERBOSE
NMA	DEBUG EIGEN ENSEMBLE JOBS KEYWORDS MUTE NMADOMAIN NMAMETHOD NMAPDB ROOT TITLE VERBOSE XYZOUT
NCS	BINS CELL COMPOSITION DEBUG HKLIN HKLOUT JOBS MACANO MACTNCS MUTE NORMALIZATION OUTLIER REFLECTIONS RESHARPEN RESOLUTION ROOT SPACEGROUP TITLE TNCS VERBOSE
EP_AUTO	ATOM BFACTOR BINS CELL CLUSTER COMPOSITION CRYSTAL DEBUG HAND HKLIN HKLOUT JOBS KEYWORDS LLGCOMPLETE LLGMAPS MACANO MACSAD MACTNCS MUTE NORMALIZATION OUTLIER PARTIAL RESHAPEN RESOLUTION RFACTOR ROOT SCATTERING SPACEGROUP TITLE TNCS TOPFILES VARSAD VERBOSE WAVELENGTH XYZOUT
MR_ATOM	ATOM CELL COMPOSITION CRYSTAL DEBUG ELLG ENSEMBLE HKLIN HKLOUT JOBS KEYWORDS LLGCOMPLETE LLGMAPS MACANO MACMR MACSAD MACTNCS MUTE NORMALIZATION PACK PEAKS PERMUTATIONS PURGE REFLECTIONS RESCORE RESOLUTION RFACTOR ROOT SAMPLING SEARCH SGALTERNATIVE SOLUTION SPACEGROUP TITLE TNCS TOPFILES VERBOSE XYZOUT ZSCORE