Comparing related structures and viewing the structures in the context of sequence alignments are important tasks in protein structure-function research. While many programs exist for individual aspects of such work, there is a need for interactive visualization tools that provide a deep integration of sequence and structure, help in changing data of one type based on the other or adjusting a sequence alignment based on spatial fit or can be used with a researcher's own data etc.
The molecular graphics program UCSF Chimera have a suite of tools for interactive analyses of sequences and structures and for the interactive visualization and analysis of molecular structures and related data, including density maps, trajectories, supramolecular assemblies, conformational ensembles, docking results and sequence alignments. High-quality images and animations can be generated. Chimera includes complete documentation and is free of charge for academic, government, nonprofit, and personal use. Structures automatically associate with sequences in imported alignments, allowing many kinds of crosstalk.
Besides supporting core visualization, the software is specifically designed for extensibility, to allow outside developers to incorporate new desirable functions.
Chimera can read molecular structures and associated data in a large number of formats, display the structures in a variety of representations, and generate high-quality images and animations suitable for publication and presentation.
High-quality images and movies can be created.
Chimera is developed by the Resource for Biocomputing, Visualization, and Informatics
automatic identification of atom
hydrogen addition and partial charge assignment
high-quality hydrogen bond, contact, and clash detection
measurements of 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 (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 and fetch from Protein Data Bank, CATH or SCOP (domains), 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
visual effects including depth-cueing, interactive shadows, silhouette edges, multicolor backgrounds
standard molecular representations (sticks, spheres, ribbons, molecular surfaces)
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 (see below)
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