Modes

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Revision as of 13:35, 3 May 2012 by Airlie (talk | contribs)

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. The mode of operation is controlled with the MODE keyword.

  • Automated Molecular Replacement
    Mode MR_AUTO combines anisotropy correction, cell content analysis, fast rotation and translation functions, and refinement and phasing to automatically solve a structure by molecular replacement
  • Fast Rotation Function
    Mode MR_FRF combines the anisotropy correction and likelihood-enhanced fast rotation function, by default rescored with the full rotation likelihood function,.
  • Fast Translation Function
    Mode MR_FTF combines the anisotropy correction and likelihood-enhanced fast translation function, by default rescored by the full likelihood translation function.
  • Brute Rotation Function
    Mode MR_BRF combines the anisotropy correction and a brute-force search of angles using the full likelihood rotation function.
  • Brute Translation Function
    Mode MR_BTF combines the anisotropy correction and a brute force search of positions using the full likelihood translation function to find the position of a previously oriented model.
  • Packing
    Mode MR_PAK determines whether molecular replacement solutions pack in the unit cell using a C-alpha clash test.
  • Log-Likelihood Gain
    Mode MR_LLG combines the anisotropy correction and the likelihood function to calculate the log-likelihood gain for full or partial molecular replacement solutions.
  • Refinement and Phasing
    Mode MR_RNP combines the anisotropy correction 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.
  • 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.
  • 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.
  • 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.
  • Automated Experimental Phasing
    Mode EP_AUTO combines anisotropy correction, cell content analysis, and SAD phasing to automatically solve a structure by experimental phasing
  • SAD Phasing
    Mode EP_SAD refines atoms using the SAD likelihood function, and completes the structure with log-Likelihood gradient maps.



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 TNCS 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
TNCS BINS CELL COMP DEBU HKLI HKLO JOBS MACA MACT MUTE NORM OUTL REFL RESH RESO ROOT SPAC TITL TNCS VERB