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