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
Famous quotes containing the words general, structure and/or analysis:
“He who never sacrificed a present to a future good or a personal to a general one can speak of happiness only as the blind do of colors.”
—Olympia Brown (1835–1900)
“There is no such thing as a language, not if a language is anything like what many philosophers and linguists have supposed. There is therefore no such thing to be learned, mastered, or born with. We must give up the idea of a clearly defined shared structure which language-users acquire and then apply to cases.”
—Donald Davidson (b. 1917)
“Whatever else American thinkers do, they psychologize, often brilliantly. The trouble is that psychology only takes us so far. The new interest in families has its merits, but it will have done us all a disservice if it turns us away from public issues to private matters. A vision of things that has no room for the inner life is bankrupt, but a psychology without social analysis or politics is both powerless and very lonely.”
—Joseph Featherstone (20th century)