Difference between revisions of "Single Atom Molecular Replacement"

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Single Atom Molecular Replacement (SAMR) with Phaser combines the MR and SAD phasing modes to solve high resolution structures. Firstly, single atoms are used for MR in the MR_AUTO mode. Then log-likelihood gradient completion is performed with EP_AUTO. The anomalous differences are not used in this step, only the mean structure factors. These two functionalities are wrapped in the MR_ATOM mode of phaser.  
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Single Atom Molecular Replacement (MODE MR_ATOM) with Phaser combines the MR and SAD phasing modes to solve high resolution structures. Firstly, single atoms are used for MR in the MR_AUTO mode. Then log-likelihood gradient completion is performed with EP_AUTO. The anomalous differences are not used in this step, only the mean structure factors. These two functionalities are wrapped in the MR_ATOM mode of phaser.  
  
 
SAMR is called from the phaser executable with the MR_ATOM mode
 
SAMR is called from the phaser executable with the MR_ATOM mode

Latest revision as of 15:01, 20 November 2014

Single Atom Molecular Replacement (MODE MR_ATOM) with Phaser combines the MR and SAD phasing modes to solve high resolution structures. Firstly, single atoms are used for MR in the MR_AUTO mode. Then log-likelihood gradient completion is performed with EP_AUTO. The anomalous differences are not used in this step, only the mean structure factors. These two functionalities are wrapped in the MR_ATOM mode of phaser.

SAMR is called from the phaser executable with the MR_ATOM mode

MODE MR_ATOM

SAMR is called from the python interface with the runMR_ATOM function

 ResultEP r = runMR_ATOM(i=InputMR_ATOM)


The first part of the algorithm is to find the heaviest atoms by MR. Enter a standard MR_AUTO script with the number of search atoms set to the number of atoms of your heaviest atom type.

MODE MR_ATOM
HKLIN tryparedoxin_peak_withfc.mtz 
LABIN F(+)=F_peak(+)  SIGF(+)=SIGF_peak(+)  F(-)=F_peak(-)  SIGF(-)=SIGF_peak(-)  
WAVELENGTH 0.98
ENSEMBLE atom ATOM SE
SEARCH ENSEMBLE atom NUM 10
COMPOSITION PROTEIN SEQ tryparedoxin.seq NUMBER 1
LLGC COMPLETE ON
LLGC ELEMENT N