e2refinetofrealign

--version

bool

show program's version number and exit

-h

--help

bool

show this help message and exit

--fbeaut

bool

(T/F)Apply extra real space symmetry averaging and masking to beautify final map prior to output

--fcref

bool

(T/F)Apply FOM filter to final reconstruction using function SQRT(2.0*FSC/(1.0+FSC))

--ifsc

string

(0,1,2,3)Calculation of FSC Table (1,2,3 save reduce memory usage): 0 = Internally calculate two reconstructions with odd and even particles and generate FSC table at end. 1 = Only use odd particles for one reconstruction. 2 = Only use even particles for one reconstruction. 3 = use all particles but only for one reconstruction.

--fstat

bool

(T/F)Calculate additional statistics in resolution table at end (QFACT, SSNR, CC, etc.). T Uses more than 50% more memory.

--iblow

string

(1,2,4)Padding factor for reference structure. 4 uses the most memory but is the fastest search and refinement

--mask

float

Size of mask radius (RO). Default is 3/8 the particle radius * its angstrom per pixel

--rrec

string

Resolution of reconstruction in angstroms. It is the resolution to which the reconstruction is calculated.

--reslow

float

Resolution of the data included in the alignment. This is the low resolution value. ex:200

--reshigh

float

Resolution of the data included in the alignment. This is the high resolution value. ex:25

--refdef

bool

FreAlign will refine the defocus

--refastyg

bool

FreAlign will refine the astigmatism

--refpart

bool

FreAlign will refine the defocus for individual particles

--thresh

float

Phase Residual cutoff. Particles with a higher phase residual will not be included in the refinement

--pbc

float

Phase Residual/Pseudo B-Factor Constant