symAxisSearch

This program is used to iteratively search for the local rotation symmtry axis

symAxisSearch <map> <n> <sym coeff file> [outmap=<file.mrc>] [maskout=<output MRC file>] [symrad=<pixels>] [srchrad=<pixels>] [thresh=<min sym coeff>] [zslice=<z0,z1>] [start=<x,y>] [convergat=<degrees,pixels>] [cpu=<n>] [verbose]

Parameters:


<map>input 3D map with the symmetry axis nearly along Z-axis
<n>the rotation symmetry
<sym coeff file>the list of symmetry coeffecients at different slices along the axis
[outmap=<file.mrc>]output the 3D map that trasnformed to let the symmetry axis along the Z-axis and through the map center (nx/2,ny/2,nz/2)
[maskout=<output MRC file>]after searching the symmetry axis, mask out the symmtric voxels above certain threshold
[symrad=<pixels>]radius of the symmtric region
[srchrad=<pixels>]radius of search region
[thresh=<min sym coeff>]minimal symmetry coeff to be included in axis fitting and density masking
[zslice=<z0,z1>]slices to search
[start=<x,y>]start axis position in xy plane, in pixel
[convergat=<degrees,pixels>]the criterion to stop the iterative search, default to 1 degree and 1 pixel
[cpu=<n>]number of CPUs to use. parallelized with OpenMP
[verbose]if set, intermediate results are outputed

Usage:

symAxisSearchOMP map.mrc 3 sym-coeff.dat cpu=4 start=60,66 thresh=0.8 zslice=30,92 maskout=map-masked.mrc outmap=map-sym.mrc

Description

This program will take the input 3D map, assuming the rotation symmetry axis is near the Z axis, find the best symmetry center in each slice, least-square-fit to a straight line to determine the direction and position of the symmetry axis.

The parallelization is done with OpenMP, which means it only work on shared memory systems. This is not compiled by default.


EMAN Manual page, generated Tue Oct 8 21:38:48 2002