scipion logo

Symmetries

Overview

This page describes the different symmetries that a polyhedron with fixed center may have and the symmetry conventions followed by Scipion. There are five fundamental symmetry classes: cyclical, dihedral, tetrahedral, octahedral and icosahedral.

For each type we show in this page:

  • Surface rendering of a volume that displays the symmetry.
  • Atomic structure file (pb format) containing an atomic structure that satisfies the symmetry. (The PDB files may be visualized with viewers such as Chimera. Link to chimera axis file).
  • Definition including the elements of symmetry.
  • X, Y and Z axes are colored in red, yellow and blue respectively.

Note: Is really hard to see the difference symmetries just looking to the images, instead download the PDB files, the axis.bild file and visualize them in chimera. In chimera command line type “represent sphere” to increase the atoms size.

Cyclic of order N (Cn)

Definition: N rotations of magnitude 360/N degrees around an axis.

Scipion Definition (CN): rotation axis = Z axis.

PDB: link to C7 model

c7 symmetry image

Dihedral of order N (Dn)

Definition: N rotations of magnitude 360/N degrees around an axis followed by a 180 rotation around a second axis. Both axes are perpendicular.

Scipion Definition (DNx): first axis = Z, second axis = X.

PDB: link to D7x model

d7x symmetry image

Scipion Definition (DNy): first axis = Z, second axis = Y.

PDB: link to D7y model

d7y symmetry image

Tetrahedral (T)

Definition: There are three orthogonal 2-fold rotation axes with in addition four 3-fold axes, centered between the three orthogonal directions

Scipion Definition (T222): two-fold symmetry axes along the X, Y, and Z axes, a three-fold along axis (1,1,1)

PDB: link to T222 model

t222 symmetry image

Scipion Definition (Tz3): a three-fold symmetry axis along Z, another three-fold axis in the YZ plane such that rotation about the X axis by ~110° is a symmetry operation

PDB: link to Tz3

tz3 symmetry image

Octahedral (O)

Definition: There are three orthogonal 4-fold rotation axes with additional four 3-fold axes, centered between the three orthogonal directions

Scipion Definition (0): 3-fold symmetry axis around (.5773502, .5773502, .5773502) 4-fold rotation axis around (0 0 1).

PDB: link to O model

o symmetry image

Icosahedral (I)

Definition: 60 elements of symmetry. 12 5-fold axes, 20 3-fold axes and 30 2-fold axes.

Scipion Definition (I222): 2-fold axes on X, Y and Z axes. With the positive Z-axis pointing at the viewer, the front-most 5-fold vertices are in YZ plane, and the front-most 3-fold axis is in the XZ plane. As known as no Crowther 222, standard in Heymman et al 2005 article).

PDB: link to I222 model

i222 symmetry image

Scipion Definition (I222r): 2-fold axes on X, Y and Z axes. With the positive Z-axis pointing at the viewer, the front-most 5-fold vertices are in XZ plane, and the front-most 3-fold axis is in the YZ plane. As known as no Crowther 222, standard in Heymman et al 2005 article).

PDB: link to I222r model

i222r symmetry image

Scipion Definition (In25): 5fold axis in Z and 2-fold in Y. With the positive Z-axis pointing at the viewer and without taken into account the 5-fold vertex in Z, there is one of the front-most 5-fold vertices in -XZ plane (note the minus X)

PDB: link to In25 model

in25 symmetry image

Scipion Definition (In25r): 5fold axis in Z and 2-fold in Y. With the positive Z-axis pointing at the viewer and without taken into account the 5-fold vertex in Z, there is one of the front-most 5-fold vertices in +*XZ* plane (note the plus X)

PDB: link to In25r model

in25r symmetry image

Scipion Definition (I2n3): 3-fold axis in Z and 2-fold in X. With the positive Z-axis pointing at the viewer and without taken into account the 3-fold vertex in Z, there is one of the front-most 3-fold vertices in -YZ plane (note the minus Y)

PDB: link to I2n3 model

i2 symmetry image

Scipion Definition (I2n3r): 3-fold axis in Z and 2-fold in X. With the positive Z-axis pointing at the viewer and without taken into account the 3-fold vertex in Z, there is one of the front-most 3-fold vertices in +*YZ* plane (note the plu Y)

PDB: link to I2n3 model

i2n3r symmetry image