Parameters
-i <input_file>
--nref <int=1>
--ref <reference_file=>
--oroot <rootname=mlf2d>
--mirror
--fast
N_imgs*N_refs
) origin offsets that yield the maximum probability of observing each experimental image, given each of the references. In the first iterations a complete integration over all references, rotations and translations is performed for all images. In all subsequent iterations, for all combinations of experimental images, references and rotations, the probability of observing the image given the optimal origin offsets from the previous iteration is calculated. Then, if this probability is not considered "significant", we assume that none of the other translations will be significant, and we skip the integration over the translations. A combination of experimental image, reference and rotation is considered as "significant" if the probability at the corresponding optimal origin offsets is larger than C times the maximum of all these probabilities for that experimental image and reference (by default C=1e-12) This version may run up to ten times faster than the original, complete-search approach, while practically identical results may be obtained. --thr <N=1>
--no_ctf <pixel_size=1>
Additional options
--eps <float=5e-5>
--iter <int=100>
--psi_step <float=5.>
--noise <float=1>
--offset <float=3.>
--frac <docfile=>
-C <double=1e-12>
--zero_offsets
--restart <iter=1>
--fix_sigma_noise
--fix_sigma_offset
--fix_fractions
--student <df=6>
--norm
--save_memA
--save_memB
--search_shift <int=3>
--reduce_snr <factor=1>
--not_phase_flipped
--ctf_affected_refs
--limit_resolution <first_high=0> <high=0> <low=999>
--fix_high <float=-1>
--include_allfreqs