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
- amino acid rotamer libraries, protein Ramachandran plot
- structure building and bond rotation
- molecular dynamics trajectory playback (many formats), distance and angle plots
- morphing between conformations of a protein or even different proteins
- display of attributes (B-factor, hydrophobicity, etc.) with colors, radii, "worms"
- easy creation of custom attributes with simple text file inputs
- ViewDock tool to facilitate interactive screening of docking results
- rich set of commands, powerful specification syntax
- many formats read, PDB and Mol2 written
- web fetch from Protein Data Bank, EDS (density maps), EMDB (density maps), ModBase (comparative models), CASTp (protein pocket measurements), Pub3D (small molecule structures), VIPERdb (icosahedral virus capsids), UniProt (protein sequences with feature annotations), others
Read more about this topic: UCSF Chimera
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