ALIGN3D

 

Align one 3d model to another.


Usage
align3d <fixed input> <free input> <output> [dot] [p3d] [refine] [checkflip] [saveref]
 
<fixed input> reference model that <free input> is aligned to.
<free input> model to be aligned to <fixed input>
<output> output file, may be the same as <free input>
dot normally similarity between models is defined as the standard deviation of the difference of the 2 models. This will cause a dot product to be used for comparisons instead.
p3d generates a text file containing the similarity value for a range of possible orientations. Useful for looking for symmetry and for deciding how robust the alignment is.
refine used when <free input> is within 10-20 degrees of being properly aligned to <fixed input>. The orientation needs only slight refinement.
checkflip sometimes the 3d models may have different handedness. This will allow <free input> to be flipped as well as rotated/translated.
saveref not usually used. This causes the 3d translational invariants used for rotational alignment to be saved to a pair of output files.

Typical Usage
align3d threed.0a.mrc threed.4.mrc threed.4a.mrc dot

Description
This program will take one 3d model and optimally align it to another 'reference' model. Currently this is done in 2 stages. First a set of translational invariants is generated from the initial models. These are then rotationally aligned using a progressive grid search algorithm. Once the rotational alignment is known, translational alignment is performed with a standard cross correlation function. Note that the grid search algorithm could potentially miss the correct orientation with complex models. Eventually rotational alignment should be rewritten using rotational cross-correlation.

The 'dot' option will provide better results for some models, worse for others. The only way to know is to try.
 

EMAN Copyright 1997-8 Steve Ludtke, Phil Baldwin