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sxmeridien - 3D Refinement: Performs 3D structure refinement. sxmeridien - 3D ML Refinement: Performs 3D Maximum Likelihood-based structure refinement.
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''usage in command line''

sxmeridien.py stack output_directory initial_volume --radius=particle_radius --outlier_percentile=outlier_percentile --ref_a=S --sym=c1 --startangles --restrict_shifts=restriction --local_filter --smear --sausage --inires --mask3D --CTF --function=user_function

=== Typical usage ===

sxmeridien exists only in MPI version.

'''mpirun -np 88 --host n2,n7,n8,n9,n10,n0,n1,n6,n3,n4,n5 sxmeridien.py bdb:data refinementdir outdir_rviper/main001/run007/ref_clip.hdf --CTF --radius=28 > cou &'''

== Input ==
    stack:: name of input stack: (default required string)
    initial_volume:: initial 3D structure: (default required string)
    radius:: particle radius: radius of the structure in pixels. if not sure, set to boxsize/2-2 (default -1)
    outlier_percentile::percentile above which outliers: are removed every iteration. (default 95.0)
    CTF:: Use CTF: (default False)
    ref_a::method for generating the quasi-uniformly distributed projection directions: (default S)
    sym:: point-group symmetry of the structure: cn, dn, where n is multiplicity (for example c5 or d3). (default c1)
    startangles:: Use orientation parameters in the input file header: to jumpstart the procedure (default False)
    restrict_shifts:: Restrict initial searches for translation: unit - original size pixel. By default, no restriction. (default -1)
    local_filter:: Use local filtration: By default, uses generic tangent filter. (default False)
    smear:: Use rotational smear: (default False)
    sausage:: Sausage-making filter: (default False)
    inires:: initial resolution: of the initial_volume: unit - angstroms.(default 25.0)
    mask3D:: 3D mask: that defines outline of the structure, preferable with soft edges if not given, set to spherical mask with radius boxsize/2-1. (default none)

    * The remaining parameters are optional.
    function:: name of the reference preparation function: (default do_volume_mrk02)

== Output ==
    output_directory:: output folder: (default current directory)

= Description =
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 alpha:: in development  alpha:: works reasonably well


sxmeridien - 3D ML Refinement: Performs 3D Maximum Likelihood-based structure refinement.



Author / Maintainer

Pawel A. Penczek


category 1



See also

References to relevant other routines.


works reasonably well

sxmeridien (last edited 2018-07-23 18:51:48 by penczek)