Sirius contains a full-featured molecular dynamics (MD) visualizing component. It can read output files from [[AMBER]] and [[CHARMM]] simulations, including compressed and AMBER out files. [[RMSD]] changes along the trajectory can be calculated using user-defined atom subsets and displayed in an interactively updated graph. In order to reduce memory requirements, large multifile simulations may be loaded in a buffered mode. If a simulation involves changes in [[protein]] fold, Sirius can be set to track and recompute displayed [[secondary structure]] features in real time, which provides a convenient way to observe transformations of the structure. The full trajectory or selected frames can be exported as [[QuickTime]] video or a set of [[POV-Ray]] scene snapshots that can later be converted to a high quality movie.
