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Manpage of findNFoldAxisAlong
findNFoldAxisAlong
Section: User Commands (1)
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NAME
findNFoldAxisAlong  search for nfold axes after projection.
SYNOPSIS
findNFoldAxisAlong fName N maxShift
findNFoldAxisAlong fName N maxShift dir
DESCRIPTION
Before applying symmetry (e.g. using modifyMotiveList), it is helpful
to transform the subvolume average or reference so that a specific
specific symmetry axis is centered and oriented along one of cardinal
axes (in PEET, typically y). Often, the necessary rotations and
translations are easily found manually using a 3dmod Slicer window, but
in some cases an automated search over translations may be useful.
Additionally, some symmetry axes... e.g. helical screw axes... may be
difficult to locate accurately until they are projected, converting
them into a rotational symmetry axis.
FindNFoldAxesAlong will project an MRC volume along a specified axis,
apply a Gaussian mask to minimize edge effects, and search over
translations in the remaining 2 axes for shifts which maximize
crosscorrelation between the shifted image and the one with C<N>
symmetry applied.
Note that shifts are applied in Fourier space with wraparound, so
a crystallographic... i.e. infinitely repeating... structure is assumed.
When this is not appropriate, padding the original image may be required.
Additionally, at present findNFoldAxisAlong currently can only project
along and search for symmetry axes parallel to the cardinal axes of
the input volumes. Rotation to handle nonaligned axes should be handled
externally before calling this program
 fName

The file name of the MRC volume to process.
 N

The order or the expected rotational symmetry axis. E.g. 2 specifies
a 2fold (C2) rotational symmetry axis.
 maxShift

An integer specifying the maximum pixel shift along each of the 2
remaining axes.
 dir

The direction (1=x, 2=y, 3=z, default=2) along which the volume will
be projected and parallel to which the symmetry axis will lie.
AUTHORS
John Heumann
SEE ALSO
PEET(1) and modifyMotiveList(1)
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 SYNOPSIS

 DESCRIPTION

 AUTHORS

 SEE ALSO

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Time: 18:16:05 GMT, January 11, 2021