= align3d =
 ''Rotational and translational alignment of 3d models''

== Usage ==
 align3d <fixed input> <input> <output> [checkflip] [trans] [refine] [slow] [noshrink] [p3d] [saveref] [precen]

=== Parameters ===
 || <fixed input>||The reference to align to||
 || <input>||Volume to be aligned||
 || <output>||Aligned output||
 ||[checkflip]||Allow for possible handedness difference between models||
 ||[trans]||Do a translational alignment at the end. Works better if models are precentered||
 ||[refine]||Assumes the models are already within a few degrees of proper alignment||
 ||[slow]||For models that seem to be difficult to align, this will search with a finer angular step||
 ||[noshrink]||Normally the models are scaled down by a factor of 2 for faster alignment. This causes the full sized model to be used.||
 ||[p3d]||Generate a 3d dataset containing the correlations vs the 3 euler angles||
 ||[saveref]||Experimental||
 ||[precen]||Experimental||
 Typical usage: align3d <fixed input> <free input> <output> [p3d] [refine] [checkflip] [saveref] [slow] [precen]

== Description ==
This program will take one 3d model and optimally align it to another 'reference' model. Rotational alignment is performed by testing all possible angles at progressively smaller angular increments. If the initial increment is too large, it may fail for some models. The slow option will reduce the initial increment to try to take care of this problem. Eventually this routine will be rewritten to use rotational cross-correlation.

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EMAN Manual page, generated Mon Jan  8 17:35:59 2007