Volume_find_symmetry_v31

!xmipp_volume_find_symmetry (v3.1)

Usage

Find a symmetry rotational axis. The output is of the form

Symmetry axis (rot,tilt)= 10 20 -->    0.33682   0.059391    0.93969

The angles represent the rot and tilt angles of the symmetry axis see the note on Euler angles convention in Xmipp). The rest of the numbers is the axis itself in X, Y, Z coordinates. In this way, the symmetry axis is a line that passes through the center of the volume and whose direction is this vector. It is important that the volume is correctly centered.

See also Volume_center_v3 Transform_geometry_v3

Parameters

$: Volume to process $`-o <file`> $`--thr <N`1> $: Symmetry mode where <mode> can be:

Locate rotational axis $--rot <rot00> <rotF=355> <step=5> $--tilt <tilt00> <tiltF=90> <step=5> $: Perform a local search around this angle $: Use cubic B-Splines for the interpolations

Locate helical parameters $-z <z01> <zF=10> <zstep=0.5> $--rotHelical <rot00> <rotF=357> <step=3> $``: Perform a local search around this angle and shift $--mask <mask_typecircular> where <mask_type> can be:

• • $--center <x00> <y0=0> <z0=0>

Examples and notes

A typical application for a rotational symmetry axis is

xmipp_volume_center -i volume.vol
xmipp_volume_find_symmetry -i volume.vol --sym rot 3

Presume the symmetry axis is in rot=20, tilt=10. To align vertically the axis use

xmipp_transform_geometry -i volume.vol --rotate euler 20 10 0

For locating the helical parameters use

xmipp_volume_find_symmetry -i volume --sym helical -z 0 6 1 --mask circular -32 --thr 2 -o parameters.xmd

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