Symmetrize

Symmetrize

Purpose

This program symmetrizes a volume according to the corresponding symmetry elements. The output can be in the same input file or in a different one.

Usage

$ symmetrize ...

Paramteres

• `` Name of the input volume to be symmetrized
• `` Name of the symmetrized output file (optional, if you don´t provide it the input file will be rewritten)
• `` File with the symmetry elements or point group acronym. See below for a description
• `` By default, the volume is wrapped in all geometrical operations performed. Use this option if you don't want to
• `` Use cubic B-splines for all interpolations, otherwise trilinear interpolations are performed.

Structure of the Symmetry File

# The fold is the number of times that the volume can be rotated along
# the symmetry axis giving the same view from different view points.
# the structure for the rotational axis is
# rot_axis      <fold> <X0> <Y0> <Z0>
# mirror_plane         <X0> <Y0> <Z0>
# P4212
# inversion
# The following line is a 6-fold rotational symmetry axis along Z-axis.
rot_axis      6 0 0 1
mirror_plane    0 0 1

Point group acronyms

Point groups and their acronyms are described at http://xmipp.cnb.csic.es/twiki/bin/view/Xmipp/Symmetry

Valid (case-insensitive) acronyms are:

• C1
• Ci
• Cs
• Cn(from here onn must be an integer number with no more than 2 digits)
• Cnv
• Cnh
• Sn
• Dn
• Dnv
• Dnh
• T
• Td
• Th
• O
• Oh
• I
  • I1 (alternative notation I)
  • I2
  • I3
  • I4
  • I5
• Ih

Examples and notes

Symmetrize leaving the input volume untouched

$ symmetrize -i volume.vol -o volumesym.vol -sym symmetry.sym

Alternative using point group acronym for c6 symmetry

$ symmetrize -i volume.vol -o volumesym.vol -sym c6

Symmetrize leaving the output in the same place as the input volume

$ symmetrize -i volume.vol -sym symmetry.sym

--Main.AlfredoSolano - 23 Jan 2007