Sirius contains a full-featured molecular dynamics (MD) visualization 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.
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