UCSF Chimera (or simply Chimera) is an extensible program for

interactive visualization Visualization or visualisation (see spelling differences) is any technique for creating images, diagrams, or animations to communicate a message. Visualization through visual imagery has been an effective way to communicate both abstract and c ...

and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and

conformational ensembles In computational chemistry, conformational ensembles, also known as structural ensembles, are experimentally constrained computational models describing the structure of intrinsically unstructured proteins. Such proteins are flexible in nature, ...

. 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 land-grant research university in San Francisco, California. It is part of the University of California system and is dedicated entirely to health science and life science. It cond ...

. Development is partially supported by the

National Institutes of Health The National Institutes of Health, commonly referred to as NIH (with each letter pronounced individually), is the primary agency of the United States government responsible for biomedical and public health research. It was founded in the late ...

(NIGMS grant P41-GM103311). The next-generation program is UCSF ChimeraX.

General structure analysis

* automatic identification of atom * hydrogen addition and partial charge assignment * high-quality

hydrogen bond In chemistry, a hydrogen bond (or H-bond) is a primarily electrostatic force of attraction between a hydrogen (H) atom which is covalently bound to a more electronegative "donor" atom or group (Dn), and another electronegative atom bearing a ...

, 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 region ...

, protein contact map * structure building and bond rotation *

molecular dynamics Molecular dynamics (MD) is a computer simulation method for analyzing the 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 dynamic "evolution" of the ...

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. The data, typically obtained by X-ray crystallography, NMR spectroscopy, or, increasingly, cry ...

, CATH or

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 designa ...

(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 from ...

(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 The Persistence of Vision Ray Tracer, most commonly acronymed as POV-Ray, is a cross-platform ray-tracing program that generates images from a text-based scene description. It was originally based on DKBTrace, written by David Kirk Buck and Aaro ...

* scene export to

X3D X3D is a royalty-free ISO/IEC standard for declaratively representing 3D computer graphics. File format support includes XML, ClassicVRML, Compressed Binary Encoding (CBE) and a draft JSON encoding. X3D became the successor to the Virtual Re ...

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, or evolutionary relationships between the sequences. Alig ...

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 Blast or The Blast may refer to: * Explosion, a rapid increase in volume and release of energy in an extreme manner *Detonation, an exothermic front accelerating through a medium that eventually drives a shock front Film * ''Blast'' (1997 film) ...

search via Web service *

multiple sequence alignment Multiple sequence alignment (MSA) may refer to the process or the result of sequence alignment of three or more biological sequences, generally protein, DNA, or RNA. In many cases, the input set of query sequences are assumed to have an evolutio ...

via Clustal Omega and

MUSCLE Skeletal muscles (commonly referred to as muscles) are organs of the vertebrate muscular system and typically are attached by tendons to bones of a skeleton. The muscle cells of skeletal muscles are much longer than in the other types of muscl ...

Web services * interfaces to

MODELLER Modeller, often stylized as MODELLER, is a computer program used for homology modeling to produce models of protein tertiary structures and quaternary structures (rarer). It implements a method inspired by nuclear magnetic resonance spectroscopy ...

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