Xmipp

xmipp_volume_find_symmetry (v3.0)

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 transform_geometry

Parameters

-i <volumeFile>
Volume to process
-o <file=>
Metadata with the orientation of the symmetry axis In helical mode, there is a file called output.xmp with the correlation map (vertical axis is the rotation, horizontal axis is the translation)
--thr <N=1>
Number of threads
--sym <mode>
Symmetry mode
where <mode> can be:
  • rot <n> Order of the rotational axis
  • helical Helical symmetry.

Locate rotational axis

--rot <rot0=0> <rotF=355> <step=5>
Limits for rotational angle search
--tilt <tilt0=0> <tiltF=90> <step=5>
Limits for tilt angle search
--localRot <rot0> <tilt0>
Perform a local search around this angle
--useSplines
Use cubic B-Splines for the interpolations

Locate helical parameters

-z <z0> <zF> <zstep>
Search space for the shift in Z
--rotHelical <rot0=0> <rotF=355> <step=5>
Search space for rotation around Z
--localHelical <rot0> <z0>
Perform a local search around this angle
--mask <mask_type=circular>
Restrict the comparison to the mask area.
where <mask_type> can be:
  • circular <R> circle/sphere mask if R>0 => outside R if R<0 => inside R
  • DWT_circular <R> <smin> <smax> circle/sphere mask smin and smax define the scales to be kept
  • rectangular <Xrect> <Yrect> <Zrect=-1> 2D or 3D rectangle if X,Y,Z > 0 => outside rectangle if X,Y,Z < 0 => inside rectangle
  • crown <R1> <R2> 2D or 3D crown if R1,R2 > 0 => outside crown if R1,R2 < 0 => inside crown
  • cylinder <R> <H> 2D circle or 3D cylinder if R,H > 0 => outside cylinder if R,H < 0 => inside cylinder
  • cone <theta> 3D cone (parallel to Z) if theta > 0 => outside cone if theta < 0 => inside cone
  • wedge <th0> <thF> 3D missing-wedge mask for data collected between tilting angles th0 and thF (around the Y-axis)
  • binary_file <binary_file> Read from file
--center <x0=0> <y0=0> <z0=0>
mask center

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 -6 6 1 --mask circular -32 --thr 2 -o parameters.xmd

User's comments

%COMMENT{type="tableappend"}%