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Name

sxmeridien - 3D Refinement: Performs 3D structure refinement.

Usage

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

    Author / Maintainer

    Pawel A. Penczek

    Keywords

    category 1
    APPLICATIONS

    Files

    sxmeridien.py

    See also

    References to relevant other routines.

    Maturity

    alpha
    in development

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