Content-type: text/html Manpage of findNFoldAxisAlong

findNFoldAxisAlong

Section: User Commands (1)
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NAME

findNFoldAxisAlong - search for n-fold 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 cross-correlation 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 non-aligned 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 2-fold (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)


 

Index

NAME
SYNOPSIS
DESCRIPTION
AUTHORS
SEE ALSO

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