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 The University of California, San Francisco (UCSF) is a Public university, public Land-grant university, land-grant research university in San Francisco, California, United States. It is part of the University of California system and is dedic ...

. Development is partially supported by the

National Institutes of Health The National Institutes of Health (NIH) is the primary agency of the United States government responsible for biomedical and public health research. It was founded in 1887 and is part of the United States Department of Health and Human Service ...

(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 Chimera is no longer actively developed and is superseded by UCSF ChimeraX.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 In chemistry, a hydrogen bond (H-bond) is a specific type of molecular interaction that exhibits partial covalent character and cannot be described as a purely electrostatic force. It occurs when a hydrogen (H) atom, Covalent bond, covalently b ...

, 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 In biochemistry, a Ramachandran plot (also known as a Rama plot, a Ramachandran diagram or a �,ψplot), originally developed in 1963 by G. N. Ramachandran, C. Ramakrishnan, and V. Sasisekharan, is a way to visualize energetically allowed regio ...

, protein contact map * structure building and bond rotation *

molecular dynamics Molecular dynamics (MD) is a computer simulation method for analyzing the Motion (physics), physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the 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 The Protein Data Bank (PDB) is a database for the three-dimensional structural data of large biological molecules such as proteins and nucleic acids, which is overseen by the Worldwide Protein Data Bank (wwPDB). This structural data is obtained a ...

CATH Cath may refer to: __NOTOC__ People * Cath Bishop (born 1971), British former rower and 2003 world champion * Cath Carroll (born 1960), British musician and music journalist * Cath Coffey (), one of the earliest members of British rap band Stereo ...

SCOP A ( or ) was a poet as represented in Old English poetry. The scop is the Old English counterpart of the Old Norse ', with the important difference that "skald" was applied to historical persons, and scop is used, for the most part, to designat ...

(domains), EDS (density maps), EMDB (density maps), ModBase (comparative models), CASTp (protein pocket measurements), Pub3D (small molecule structures), VIPERdb (icosahedral virus capsids),

UniProt UniProt is a freely accessible database of protein sequence and functional information, many entries being derived from genome sequencing projects. It contains a large amount of information about the biological function of proteins derived fro ...

(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 In bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural biology, structural, or evolutionary relationships between ...

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 Muscle is a soft tissue, one of the four basic types of animal tissue. There are three types of muscle tissue in vertebrates: skeletal muscle, cardiac muscle, and smooth muscle. Muscle tissue gives skeletal muscles the ability to muscle contra ...

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 *

and CDD feature annotations shown as colored boxes on sequences * trees in Newick format read/displayed

References

External links