Single Atom Molecular Replacement

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.

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