projecticos

This program is used to project icosahedral 3D map into the asymmetric unit

projecticos <map> [inort=<ortfile>] [inort2=<IMAGIC file>] [out=<filename>] [vert=<0-11>] [ori5f=<0-4>] [from2forigin] [mask=<radius>] [imask=<radius>] [invert] [pad=<newsize>] [clip=<newsize>] [text[=<orient file>]] [path=<path>] [<step=stepsize(indegree)] [wave] [MRCcenter] [mode=<1-6>] [cpu=<n>] [frac=<0 to d-1>/<d>] [verbose]

Description

This program will take the input icosahedral 3D map oriented as 5fold map(z at 5f, y at 2f) or 2fold map (xyz all at 2f) and project into the icosahedral asymmetric unit (standard MRC convention) at specified step (even change for alt and az).

Parameters:


<map>input file, single 3D map, usually 5fold map, or could be the 2fold map at orientation origin
[inort=<ortfile>]input orientation file in MRC data file format
[inort2=<IMAGIC file>]input orientation from IMAGIC file header
[out=<filename>]output imagic file name, default to proj.img
[vert=<0-11>]to pre-rotate such that the tail(assume on +z axis for 5fold map) was originally on specified vertex, ignored if "from2forigin" is set
[ori5f=<0-4>]to pre-rotate such that the tail(assume on +z axis for 5fold map) was originally at one of the 5 azimuthal orientations, ignored if "from2forigin" is set
[from2forigin]if set, then the input map is already oriented at orientation origin (xyz all at 2fold axis)
[mask=<radius>]in pixel, the maximal radius to include
[imask=<radius>]in pixel, the minimal radius to include
[invert]the projetion density will be inverted (e.g. multiply by -1)
[pad=<newsize>]pad the size of 3D map before projecting
[clip=<newsize>]the size of final output 2D image (square)
[text[=<orient file>]]if the orientation/center parameter file in MRC convention is output, default to "Icos_projectOrtCenter.dat"
[path=<path>]if set, the path will be written before the filename in above parameter file
[<step=stepsize(indegree)]step size in degree, default to 2 degree
[wave]output will be wavelet transformed and size would be shrunk by 2
[MRCcenter]will shift the center in projections from (nx/2,ny/2) to (nx/2-1,ny/2-1)
[mode=<1-6>]projection mode, 1-6 use FFT slice technique, default (-1) to slow but good real space technique
[cpu=<n>]number of CPUs to use. parallelized with OpenMP
[frac=<0 to d-1>/<d>]for runpar parallelization, current process in total processes
[verbose]if set, intermediate results are outputed

Usage:

projecticos map.mrc step=4 from2forigin

projecticos map.mrc step=4 vert=2 verbose frac=1/4

Description


EMAN Manual page, generated Tue Oct 8 21:50:26 2002