UCSF Chimera

UCSF Chimera

File:Chimera1.png Chimera main window (FSH and receptor, 1xwd) and sequence window (alignment of FSH receptors from different species).
Developer(s)	Resource for Biocomputing, Visualization, and Informatics (RBVI), UCSF
Stable release	1.4 / December 3, 2009
Operating system	Windows, Mac OS X, Linux
Type	Molecular modelling
License	free for noncommercial use
Website	www.cgl.ucsf.edu/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 NIH National Center for Research Resources (grant P41-RR01081).

General Structure Analysis

• automatic atom type identification
• hydrogen addition and partial charge assignment
• high-quality hydrogen bond, contact, and clash detection
• distance and angle measurements, rotatable bonds
• amino acid rotamer libraries (backbone-dependent and -independent)
• molecular dynamics trajectory playback (many formats)
• clustering of conformational ensembles
• morphing between conformations of a protein or even different proteins
• display of attributes (B-factor, hydrophobicity, etc.) with colors, radii, "worms"
• easy creation of new attributes with simple text file inputs
• rich set of commands, powerful specification syntax
• many formats read, PDB and Mol2 written
• web fetch from Protein Data Bank, PQS (predicted quaternary structure), CASTp (protein pocket measurements), EDS (density maps), ModBase (comparative models), Pub3D (small molecule structures), others

Presentation Images and Movies

• images can be saved at arbitrarily high resolution
• adjustable background color, lighting, depth-cueing, silhouette edges
• stick, ball-and-stick, sphere, ribbon, and surface displays
• nonmolecular geometric objects
• labeling with arbitrary text and symbols, color keys
• isosurfaces and transparent renderings of volume data (see below)
• 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
• alternatively, movie content and recording can be scripted
• movie recording is integrated with morphing and MD trajectory playback

Volume Data Tools

• many formats of volume data maps (electron density, electrostatic potential, others) read, several written
• interactive threshold adjustment, multiple isosurfaces (mesh or solid), 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 single data planes, optionally as topographic maps
• volume data time series playback and morphing
• many tools for segmenting and editing maps
• Gaussian smoothing, Fourier transform
• surface area and surface-enclosed volume measurements

Sequence and Structure Tools

• many sequence alignment formats read, edited, written
• automatic, mismatch-tolerant association of structures with alignment sequences
• sequence-structure crosstalk: highlighting in one highlights the other
• multiple methods for calculating conservation and displaying values on associated structures
• Newick tree format read
• protein BLAST search via Web service
• structure superposition using the associated sequence alignment
• in the absence of a pre-existing alignment, structure superposition using both residue type and secondary structure information
• generation of structure-based sequence alignments from superpositions of two or more proteins

See also

• List of molecular graphics systems
• Molecular modelling
• Molecular graphics
• Molecular dynamics
• Software for molecular mechanics modeling

External links

• UCSF Chimera home page
• Chimera Image Gallery and Animation Gallery
• papers about Chimera
• Resource for Biocomputing, Visualization, and Informatics
• University of California, San Francisco