UCSF Chimera

General structure analysis

• automatic identification of atom
• 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, protein contact map
• structure building and bond rotation
• molecular dynamics trajectory playback, distance and angle plots
• morphing between conformations of a protein or even different proteins
• display of attributes 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 and fetch from Protein Data Bank, CATH or SCOP, EDS, EMDB, ModBase, CASTp, Pub3D, VIPERdb, UniProt, others
• interfaces to PDB2PQR charge/radius assignment, APBS electrostatics calculations, AutoDock Vina single-ligand docking

  Presentation images and movies

• high-resolution images
• visual effects including depth-cueing, interactive shadows, silhouette edges, multicolor backgrounds
• standard molecular representations
• pipes-and-planks for helices and strands; nucleotide objects including lollipops and ladder rungs
• ellipsoids to show anisotropic B-factors
• nonmolecular geometric objects
• renderings of density maps and other volume data
• labeling with text, symbols, arrows, color keys
• different structures can be clipped differently and at any angle
• optional raytracing with bundled POV-Ray
• scene export to X3D and other formats
• simple graphical interface for creating movies interactively
• scenes can be placed as keyframes along an animation timeline
• alternatively, movie content and recording can be scripted; rich set of related commands
• movie recording is integrated with morphing and MD trajectory playback

  Volume data tools

• many formats of volume data maps read, several written
• interactive threshold adjustment, multiple isosurfaces, transparent renderings
• fitting of atomic coordinates to maps and maps to maps
• density maps can be created from atomic coordinates
• markers can be placed in maps and connected with smooth paths
• display of individual data planes or multiple orthogonal planes
• volume data time series playback and morphing
• many tools for segmenting and editing maps
• Gaussian smoothing, Fourier transform, other filtering and normalization
• measurements: surface area, surface-enclosed volume, map symmetry, others

  Sequence-structure tools

• many sequence alignment formats read, written
• sequence alignments can be created, edited
• sequences automatically associate with structures
• sequence-structure crosstalk: highlighting in one highlights the other
• protein BLAST search via Web service
• multiple sequence alignment via Clustal Omega and MUSCLE Web services
• interfaces to MODELLER for homology modeling and loop building
• structure superposition with or without pre-existing sequence alignment
• generation of structure-based sequence alignments from multiple superpositions
• several methods for calculating conservation and displaying values on associated structures
• RMSD header showing spatial variability of associated structures
• user-defined headers including histograms and colored symbols
• UniProt and CDD feature annotations shown as colored boxes on sequences
• trees in Newick format read/displayed