UCSF Chimera

UCSF Chimera
UCSF Chimera
	Chimera main window (FSH and receptor, 1xwd) and sequence window (alignment of FSH receptors from different species).
Developers	Resource for Biocomputing, Visualization, and Informatics (RBVI), UCSF
Stable release	1.19 / 6 March 2025; 19 months ago
Operating system	Microsoft Windows, OS X, Linux
Type	Molecular modelling
License	Free for noncommercial use
Website	www.rbvi.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 partially supported by the National Institutes of Health (NIGMS grant P41-GM103311). Chimera is no longer actively developed and is superseded by UCSF ChimeraX.

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 (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
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 (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

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 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 (histogram above the sequences) 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

References

↑ Pettersen, EF; Goddard, TD; Huang, CC; Couch, GS; Greenblatt, DM; Meng, EC; Ferrin, TE (2004). "UCSF Chimera--a visualization system for exploratory research and analysis". J Comput Chem. 25 (13): 1605–12. CiteSeerX 10.1.1.456.9442. doi:10.1002/jcc.20084. PMID 15264254. S2CID 8747218. {{cite journal}}: Cite uses deprecated parameter |citeseerx= (help)
↑ "UCSF Chimera Home Page". www.rbvi.ucsf.edu. Retrieved 2025-04-16.
↑ Goddard, T. D.; Huang, C. C.; Meng, E. C.; Pettersen, E. F.; Couch, G. S.; Morris, J. H.; Ferrin, T. E. (2017). "UCSF chimerax: meeting modern challenges in visualization and analysis". Protein Science. 27 (1): 14–25. doi:10.1002/pro.3235. PMC 5734306. PMID 28710774.

External links

[1] Pettersen, EF; Goddard, TD; Huang, CC; Couch, GS; Greenblatt, DM; Meng, EC; Ferrin, TE (2004). "UCSF Chimera--a visualization system for exploratory research and analysis". J Comput Chem. 25 (13): 1605–12. CiteSeerX 10.1.1.456.9442. doi:10.1002/jcc.20084. PMID 15264254. S2CID 8747218. {{cite journal}}: Cite uses deprecated parameter |citeseerx= (help)

[2] "UCSF Chimera Home Page". www.rbvi.ucsf.edu. Retrieved 2025-04-16.

[3] Goddard, T. D.; Huang, C. C.; Meng, E. C.; Pettersen, E. F.; Couch, G. S.; Morris, J. H.; Ferrin, T. E. (2017). "UCSF chimerax: meeting modern challenges in visualization and analysis". Protein Science. 27 (1): 14–25. doi:10.1002/pro.3235. PMC 5734306. PMID 28710774.