make3dnonorm

This program builds 3D models from a set of class averages using Fourier techniques

make3dnonorm <input file> [out=<outfile>] [noweight] [sym=<c4,icos,etc>] [pad=<padsize>] [mode=<1-6>] [mask=<rad>] [norm] [resmap=<name>] [inorm]

Parameters:


<input file>File containing class averages
[out=<outfile>]Output 3D MRC file
[noweight]Normally the class averages are weighted by the number of raw particles used, this disables that
[sym=<c4,icos,etc>]The symmetry to apply to the model
[pad=<padsize>]To reduce Fourier artifacts, the model is typically padded by ~25%
[mode=<1-6>]Specifies the interpolation size, 2 is the default
[mask=<rad>]real-space mask radius
[norm]Normalize the slices based on associated projections in a 'classes' style file
[resmap=<name>]Generates a 'resolution map' in another 3D MRC file
[inorm]This will use a special weighting scheme to compensate for poor SNR sampling on the unit sphere

Usage:

make3d classes.1.img out=threed.1.mrc hard=25 sym=c4 pad=128 mask=42

Description

This program is virtually identical to make3d except for 3 changes. First, it has a reduced memory footprint because it doesn't keep all of the particles/class-averages in memory. Second, it only normalizes slices on request, and does so by comparing to associated class-averages. Finally, there is no mechanism for excluding 'bad' slices.

inorm can be used to compensate for cases where strange high resolution radial artifacts occur. This is generally due to nonuniform orientation distributions producing azimuthal variations in signal/noise ratio. It may have some odd noise enchancing effects, though.


EMAN Manual page, generated Wed Feb 18 10:33:43 2009