make3d

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

make3d <input file> [out=<outfile>] [hard=<maxpr>] [noweight] [sym=<c4,icos,etc>] [pad=<padsize>] [mode=<1-6>] [mask=<rad>] [keep=<sigmamult>] [resmap=<name>] [goodbad]

Parameters:


<input file>File containing class averages
[out=<outfile>]Output 3D MRC file
[hard=<maxpr>]This specifies how well the class averages must match the model to be included, 25 is typical
[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
[keep=<sigmamult>]An alternative to 'hard'
[resmap=<name>]Generates a 'resolution map' in another 3D MRC file
[goodbad]Saves the used and unused class averages in 2 files

Usage:

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

Description

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 in their headers. The 3d model building process is iterative. The iterative loop handles 2 things. First, the relative normalization of the slices is not initially known. Second, some class averages will typically be worse than others. Just like when generating class averages from individual images, the images which are the least consistent with the overall model will be excluded from the reconstruction. Similar to classalignall, a sigma multiplier may be specified for discarding individual class averages, or alternatively, a hard phase error threshold may be set. Any image with a higher phase error with the 3d model than the threshold will be discarded. Only one of these 2 options, 'keep=' or 'hard=' should be specified. The phase error should not be interpreted as a residual. Typically this value should be between 20 and 30.

'sym=' specifies the symmetry of the 3d model. If nothing is specified, the model is assumed to have no symmetry. Currently, only Cn, Dn and icos symmetries are supported.

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 Tue Feb 5 15:30:08 2002