Modes

From Phaserwiki
Revision as of 08:57, 9 December 2010 by Randy (talk | contribs) (Add WAVELENGTH to required keywords for EP_AUTO and EP_SAD)

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 Compulsory Optional Expert
MR_AUTO ENSEMBLE HKLIN LABIN MODE SEARCH COMPOSITION HKLOUT FINAL HKLOUT PACK PERMUTATIONS PURGE RESCORE RESOLUTION ROOT SCRIPT SGALTERNATIVE SOLUTION SPACEGROUP TITLE TOPFILES VERBOSE XYZOUT BINS BOXS CELL CLMN MUTE OUTLIER SAMPLING SOLPARAMS
MR_FRF ENSEMBLE HKLIN LABIN MODE SEARCH COMPOSITION FINAL RESCORE RESOLUTION ROOT SCRIPT SOLUTION SPACEGROUP TITLE TOPFILES VERBOSE XYZOUT BINS BOXS CELL CLMN MUTE OUTLIER SAMPLING SOLPARAMS TARGET
MR_BRF ENSEMBLE HKLIN LABIN MODE SEARCH COMPOSITION FINAL RESOLUTION ROOT ROTATION SCRIPT SOLUTION SPACEGROUP TITLE TOPFILES VERBOSE XYZOUT BINS BOXS CELL MUTE OUTLIER SAMPLING SOLPARAMS
MR_FTF ENSEMBLE HKLIN LABIN MODE SOLUTION COMPOSITION FINAL RESCORE RESOLUTION ROOT SCRIPT SGALTERNATIVE SPACEGROUP TITLE TOPFILES VERBOSE XYZOUT BINS BOXS CELL MUTE OUTLIER SAMPLING SOLPARAMS TARGET
MR_BTF ENSEMBLE HKLIN LABIN MODE SOLUTION COMPOSITION FINAL RESOLUTION ROOT SCRIPT SGALTERNATIVE SPACEGROUP TITLE TOPFILES TRANSLATE VERBOSE XYZOUT BINS BOXS CELL MUTE OUTLIER SAMPLING SOLPARAMS
MR_RNP ENSEMBLE HKLIN LABIN MODE SOLUTION COMPOSITION HKLOUT RESOLUTION ROOT SCRIPT SPACEGROUP TITLE TOPFILES VERBOSE XYZOUT BINS BOXS CELL MACMR MUTE OUTLIER SOLPARAMS
MR_LLG ENSEMBLE HKLIN LABIN MODE SOLUTION COMPOSITION HKLOUT RESOLUTION ROOT SCRIPT SPACEGROUP TITLE TOPFILES VERBOSE XYZOUT BINS BOXS CELL MUTE OUTLIER SOLPARAMS
MR_PAK ENSEMBLE HKLIN LABIN MODE SOLUTION PACK ROOT SCRIPT SPACEGROUP TITLE VERBOSE TOPFILES XYZOUT CELL MUTE
EP_AUTO ATOM CRYSTAL HKLIN LABIN MODE WAVELENGTH COMPOSITION HAND HKLOUT LLGCOMPLETE ROOT SCRIPT SPACEGROUP TITLE VERBOSE XYZOUT BFACTOR CELL FFTS MACSAD MUTE OUTLIER VARSAD
EP_SAD ATOM CRYSTAL HKLIN LABIN MODE WAVELENGTH HAND HKLOUT LLGCOMPLETE PART ROOT SCRIPT SPACEGROUP TITLE VERBOSE XYZOUT BFACTOR CELL FFTS MACSAD MUTE OUTLIER VARSAD
ANO HKLIN LABIN MODE ROOT SCRIPT SPACEGROUP TITLE VERBOSE CELL MACANO MUTE
CCA COMPOSITION HKLIN LABIN MODE RESOLUTION ROOT SCRIPT TITLE VERBOSE CELL MUTE
NMA ENSEMBLE MODE EIGEN NMAMETHOD NMAPDB ROOT SCRIPT TITLE VERBOSE MUTE