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_FRF

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_FTF

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.

 ResultEP r = runEP_AUTO(i=InputEP_AUTO)

Keywords Relevant to Each Mode

Mode	Relevant Keywords
MR_AUTO	BFAC BINS BOXS CELL CLMN COMP DEBU ELLG ENSE HKLI HKLO JOBS KEYW MACA MACM MACT MUTE NORM OUTL PACK PEAK PERM PTGR PURG REFL RESC RESH RESO ROOT SAMP SEAR SGAL SOLP SOLU SPAC TARG TITL TNCS TOPF VERB XYZO ZSCO
MR_FRF	BINS BOXS CELL CLMN COMP DEBU ENSE JOBS KEYW MACA MACT MUTE NORM OUTL PEAK PURG REFL RESC RESH RESO ROOT SAMP SEAR SOLP SOLU SPAC TARG TITL TNCS TOPF VERB XYZO
MR_BRF	BINS BOXS CELL COMP DEBU ENSE JOBS KEYW MACA MACT MUTE NORM OUTL PEAK PURG REFL RESH RESO ROOT ROTA SAMP SEAR SOLP SOLU SPAC TITL TNCS TOPF VERB XYZO
MR_FTF	BINS BOXS CELL COMP DEBU ENSE JOBS KEYW MACA MACT MUTE NORM OUTL PEAK PTGR PURG REFL RESC RESH RESO ROOT SAMP SEAR SGAL SOLP SOLU SPAC TARG TITL TNCS TOPF VERB XYZO ZSCO
MR_BTF	BINS BOXS CELL COMP DEBU ENSE JOBS KEYW MACA MACT MUTE NORM OUTL PEAK PTGR PURG REFL RESH RESO ROOT SAMP SEAR SGAL SOLP SOLU SPAC TITL TNCS TOPF TRAN VERB XYZO ZSCO
MR_RNP	BFAC BINS BOXS CELL COMP DEBU ENSE HKLI HKLO JOBS KEYW MACA MACT MACM MUTE NORM OUTL PTGR REFL RESH RESO ROOT SOLP SOLU SPAC TITL TNCS TOPF VERB XYZO
MR_LLG	BINS BOXS CELL COMP DEBU ENSE HKLI HKLO JOBS KEYW MACA MACT MUTE NORM OUTL PTGR REFL RESH RESO ROOT SOLP SOLU SPAC TITL TNCS TOPF VERB XYZO
MR_PAK	CELL DEBU ENSE JOBS KEYW MUTE PACK PTGR ROOT SOLU SPAC TITL TOPF VERB XYZO ZSCO
EP_AUTO	PERM SEAR SGAL SOLU PURG BFAC BINS BOXS CELL CLMN COMP DEBU ELLG ENSE HKLI HKLO JOBS KEYW MACA MACM MACT MUTE NORM OUTL PACK PEAK PTGR REFL RESC RESH RESO ROOT SAMP SOLP SPAC TARG TITL TNCS TOPF VERB XYZO ZSCO
EP_SAD	ATOM BINS BFAC CELL CLUS COMP CRYS DEBU FFTS HAND HKLI HKLO INTE JOBS KEYW LLGC MACA MACH MACS MACT MUTE NORM OUTL PART RESH RESO ROOT SCAT SPAC TITL TNCS VARS VERB WAVE XYZO
ANO	BINS CELL COMP DEBU HKLI HKLO MACA MUTE NORM RESH REFL RESO ROOT SPAC TITL VERB
CCA	CELL COMP DEBU MUTE RESO ROOT SPAC TITL VERB
NMA	DEBU EIGE ENSE JOBS KEYW MUTE NMAM NMAP ROOT TITL VERB XYZO
NCS	BINS CELL COMP DEBU HKLI HKLO JOBS MACA MACT MUTE NORM OUTL REFL RESH RESO ROOT SPAC TITL TNCS VERB