Sophia is an educational molecular simulation package. It runs as a plugin to Chimera, a molecular modeling application developed at UCSF. To run molecular simulations, Sophia uses the Molecular Modeling Toolkit (MMTK), which is embedded as a library in Chimera. ChimeraX, the next generation of Chimera, is not currently supported.

Sophia was developed on and optimized for MacOS. It’s still possible to run Sophia on Windows or Linux, but some features will not be available, like Monte Carlo and Langevin Dynamics.