Computing axes of symmetry of biological assemblies

The Symmetry Detection Extension computes the axes of symmetry of biological assemblies. It supports detection of cyclic and dihedral symmetries of any order, as well as cubic symmetries (tetrahedral, octahedral, and icosahedral). Here is an example with an icosahedral capsid 3NQ4:

Symmetries of 3NQ4

Here with 1CHP, just start the Symmetry Detection App and compute the symmetry:

1CHP symmetries

For large assemblies, automatic symmetry detection may detect several different symmetries. Click on the one that is interesting (typically the one with the higher order and a small RMSD) to visualize the axis. In this example, we use 1B4B which has a dihedral symmetry of order 3:

1B4B symmetries

Another possibility is to provide the symmetry group:

1B4B with a chosen symmetry group

Such a symmetry group has several axes which can be browsed by expanding the symmetry group. For each axis, the corresponding RMSD is computed. To visualize a particular axis, click on it in the App interface, and it becomes bold in the viewport. A double-click aligns the camera axis with the symmetry axis:

Select symmetries

If you have any questions or feedback, please use the SAMSON forum.