3D Visualization of Protein Symmetry
To facilitate the exploration of symmetry, several options are available from the 3D Jmol views of structure:
- Default Orientations: Users can toggle between canonical views of structure that highlight symmetry: sides and back, and along unique n-fold symmetry axes.
- Symmetry axes and polyhedra. Symmetry axes and symbols representing folds (dyad for 2-fold, triad for 3-fold axis, or in general a polygon for n-fold axis) can be displayed with a structure. Users can select to view the protein enclosed in a polyhedron that matches its symmetry.
- Colored by symmetry or subunit. Structures can be colored by symmetry (see the list of color schemes used), sequence (subunits with >= 95% sequence identity shown in the same color), or by subunit.
- Pseudosymmetry. The default view shows symmetry based on a 95% sequence identity threshold. Since some structures will display pseudosymmetry when using a 30% sequence identity threshold, an option lets users toggle between the two options.
To access Jmol on the RCSB PDB site, select the "View in 3D" link on any entry's Structure Summary page. Protein symmetry is calculated for all entries containing at least one protein chain, including asymmetric units and all biological assemblies (except for entries split among several PDB files due to their size).