= Name =
sxpipeline_viper_ref3d - Create 3D Reference: Prepare an initial reference for subsequent 3D refinement by cleaning up the input volume. Mainly designed to process a ''ab initio'' 3D structure (VIPER) produced by sxviper or sxrviper.


= Usage =

''usage in command line''

sxpipeline_viper_ref3d.py  input_volume  output_directory  --resample_ratio_source  --box_size  --skip_moon_elimination  --molecular_mass  --pixel_size


=== Typical usage ===

sxpipeline_viper_ref3d.py does not support MPI. 

''' sxpipeline_viper_ref3d.py  outdir_rviper/main001/average_volume.hdf  outdir_viper_ref3d  --resample_ratio_source=outdir_isac/README_shrink_ratio.txt  --box_size=64  --molecular_mass=500  --pixel_size=2.29 '''


== Input ==
    input_volume:: Input volume: Create an initial 3D reference from this volume. (default required string)

    resample_ratio_source:: Resample ratio source: To process VIPER/RVIPER volume, specify path to shrink ratio file produced by sxisac and normally called README_shrink_ratio.txt. Otherwise, enter ratio of new to old image size to resample (decimate or interpolate up) input 3D volume to change the pixel size. if < 1, the pixel size will increase and image size decrease. if > 1, the other way round. (default '1.0').
    box_size:: Particle box size [Pixels]: Original particle box size to be restored. The box size after resampling is assumed when resample_ratio != 1.0. (default 256)
    skip_moon_elimination:: Skip moon elimination: Skip to eliminate disconnected pieces (called moons here) from the volume. (default False)
    molecular_mass:: Protein molecular mass [kDa]: The molecular mass of protein. Input argument of moon elmination. (default none)
    pixel_size:: Original micrograph pixel size [A/Pixels]: Original micrograph pixel size. Input argument of moon elmination. (default -1.0)

    * The remaining parameters are optional.

== Output ==
    output_directory:: Output directory: The results will be written here. This directory will be created automatically and it must not exist previously. (default required string)


= Description =

= Method =

= Reference =


= Author / Maintainer =
Toshio Moriya

= Keywords =
 category 1:: APPLICATIONS

= Files =
sparx/bin/sxpipeline_viper_ref3d.py

= See also =
[[sxviper]]
[[sxrviper]]
[[sxisac]]

= Maturity =
 alpha::     under development

= Bugs =
Under development
