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).
<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 |
projecticos map.mrc step=4 from2forigin
projecticos map.mrc step=4 vert=2 verbose frac=1/4