A new option has been added to DENSS for enforcing dihedral symmetry in addition to the previously available cyclical symmetry option. Dihedral symmetry adds n 2-fold axes of symmetry perpendicular to each cyclical symmetry related position. By applying this additional restraint for such objects, significantly improved reconstructions can be obtained. For example, many protein tetramers, rather than possessing 4-fold cyclical symmetry (C4) will instead possess D2 dihedral symmetry. Another well-known example is GroEL, which has 14 subunits and possesses D7 symmetry.
The new dihedral symmetry option can be enabled using the -ncs_type option and setting the parameter value to “D” or “dihedral”, while using the standard -ncs option to set the cyclical n-fold symmetry. For example, bacterial L-lactate dehydrogenase, whose structure is known (PDB ID: 1LTH), is a tetramer possessing D2 dihedral symmetry. To set D2 symmetry for this tetramer, the appropriate command would be
denss.py -f 1lth.fit -ncs 2 -ncs_type D
which will apply 2-fold cyclical symmetry and in addition apply additional 2-fold symmetry perpendicular to the cyclical axis of symmetry. A single reconstruction with DENSS results in the following:
Another example mentioned above is GroEL, which exhibits D7 symmetry (PDB ID: 1SS8). Here is a single reconstruction of GroEL by applying D7 symmetry with the following command (the cyclical axis of symmetry is along the longest principle axis):
denss.py -f groel.fit -ncs 7 -ncs_type D -ncs_axis 1