make3dicos

This program builds 3D models from a set of particles with icosahedral symmetry

make3dicos <input file> [out=<outfile>] [pad=<padsize>] [proc=<nproc>]

Parameters:


<input file>File containing class averages
[out=<outfile>]Output 3D MRC file
[pad=<padsize>]To reduce Fourier artifacts, the model is typically padded by ~25%
[proc=<nproc>]Number of processors to use.

Usage:

make3dicos classes.1.img out=threed.1.mrc pad=128

Description

Experimental - works, but not perfectly. make3d is better (but much slower)

This program is used to build a 3d model from a set of projections/class averages. The individual projections must already have assigned euler angles.

Reconstructions are performed in Fourier space. This causes certain artifacts to appear in the 3d model. These artifacts can be reduced by padding the images in real space. 50% padding produces excellent results in most cases, ie - an 80x80 image would be padded to 120x120. This would be specified with 'pad=120'. 25% padding provides adequate results in most cases. The other artifact is caused by interpolation in Fourier space. 'make3d' supports 6 levels of interpolation. Type 1 is 'nearest neighbor' interpolation and is very fast, but produces significant artifacts. The default in most cases is type 2, which generally produces the best all-around results. If you have a very small number of slices, you might try mode=5. This effect can be observed qualitatively using the v4 program. This program allows you to interactively select the interpolation mode used for generating forward projections of a 3d model. The artifacts in v4 are more severe, but qualitatively similar to those produced by Fourier reconstruction.

Finally, since Fourier reconstruction DOES produce some undesirable artifacts, generally this is just used as a preliminary model. Once this model has been generated, typically this model will be improved using a real-space iterative technique. This is implimented in make3diter.


EMAN Manual page, generated Fri Feb 8 16:12:25 2002