UCSF Chimera
UCSF Chimera (or simply Chimera) is an extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality images and movies can be created. Chimera includes complete documentation and can be downloaded free of charge for noncommercial use.
Chimera is developed by the Resource for Biocomputing, Visualization, and Informatics (RBVI) at the University of California, San Francisco. Development is funded by the National Institutes of Health (NIGMS grant P41-GM103311). The next-generation program UCSF ChimeraX is under development but is not yet publicly released.
General structure analysis
automatic identification of atom types
hydrogen addition and partial charge assignment
high-quality hydrogen bond, contact, and clash detection
measurements: distances, angles, surface area, volume
calculation of centroids, axes, planes and associated measurements