Can ROTATE cluster the generated conformations?

ROTATE can combine similar conformations into classes and represent each class by a single conformation (class representative). Two different and adjustable similarity criteria can be chosen. One crierion works in Cartesian space, i.e., is based on the RMS(XYZ) (root mean square) deviation of the Cartesian coordinates of all non-hydrogen atoms of the conformations. The second criterion uses the torsion angle space to calculate whether two conformations are similar or not, i.e., the comparison is based on the RMS(TA) deviation of the torsion angles along the rotated bonds of two conformerations.
For both methods, the RMS threshold that is used to define two conformations as similar, can be chosen by the user and both methods provide a balanced sampling of the conformational space.