UCSF Chimera

UCSF Chimera is an extensible program for interactive visualization

Interactive visualization

Interactive visualization is a branch of graphic visualization in computer science that involves studying how humans interact with computers to create graphic illustrations of information and how this process can be made more efficient....

 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

University of California, San Francisco

The University of California, San Francisco is one of the world's leading centers of health sciences research, patient care, and education. UCSF's medical, pharmacy, dentistry, nursing, and graduate schools are among the top health science professional schools in the world...

. Development is funded by the NIH National Center for Research Resources

National Center for Research Resources

The National Center for Research Resources or NCRR, is a United States government agency. NCRR provides funding to laboratory scientists and researchers for facilities and tools in the goal of curing and treating diseases.-Organization and history:...

 (grant P41-RR001081).

General Structure Analysis

• automatic atom type identification
• hydrogen addition and partial charge assignment
• high-quality hydrogen bond
  Hydrogen bond
  A hydrogen bond is the attractive interaction of a hydrogen atom with an electronegative atom, such as nitrogen, oxygen or fluorine, that comes from another molecule or chemical group. The hydrogen must be covalently bonded to another electronegative atom to create the bond...
  
  , contact, and clash detection
• distance and angle measurements, rotatable bonds, including Ramachandran plot
  Ramachandran plot
  -Introduction and early history:A Ramachandran plot , originally developed in 1963 by G. N. Ramachandran C. Ramakrishnan and V...
  
   visualization
• amino acid rotamer libraries (backbone-dependent and -independent)
• analysis of metal coordination geometry
• molecular dynamics
  Molecular dynamics
  Molecular dynamics is a computer simulation of physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a period of time, giving a view of the motion of the atoms...
  
   trajectory playback (many formats)
• clustering of conformational ensembles
• morphing between conformations of a protein or even different proteins
• calculation of theoretical SAXS profiles
• 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
  Protein Data Bank
  The Protein Data Bank is a repository for the 3-D structural data of large biological molecules, such as proteins and nucleic acids....
  
  , EDS (density maps), EMDB (density maps), ModBase (comparative models), CASTp (protein pocket measurements), Pub3D (small molecule structures), VIPERdb (icosahedral virus capsids), 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
• ellipsoids to show anisotropic B-factors
• nonmolecular geometric objects
• labeling with arbitrary text, symbols, arrows, 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
  POV-Ray
  The Persistence of Vision Raytracer, or POV-Ray, is a ray tracing program available for a variety of computer platforms. It was originally based on DKBTrace, written by David Kirk Buck and Aaron A. Collins. There are also influences from the earlier Polyray raytracer contributed by its author...
  
  
• scene export to X3D
  X3D
  X3D is the ISO standard XML-based file format for representing 3D computer graphics, the successor to the Virtual Reality Modeling Language . X3D features extensions to VRML X3D is the ISO standard XML-based file format for representing 3D computer graphics, the successor to the Virtual Reality...
  
   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-Structure Tools

• many sequence alignment
  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. Aligned sequences of nucleotide or amino acid residues are...
  
   formats read, written
• sequence alignments can be created, edited
• structures automatically associate with sequences, with some mismatch tolerance
• sequence-structure crosstalk: highlighting in one highlights the other
• multiple methods for calculating conservation and displaying values on associated structures
• user-defined headers (lines above the sequences) including histograms and colored symbols
• trees in Newick format read/displayed
• protein BLAST
  BLAST
  In bioinformatics, Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences...
  
   search via Web service
• interface to MODELLER  for homology modeling
• 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 modelling
  Molecular modelling encompasses all theoretical methods and computational techniques used to model or mimic the behaviour of molecules. The techniques are used in the fields of computational chemistry, computational biology and materials science for studying molecular systems ranging from small...
  
  
• Molecular graphics
  Molecular graphics
  Molecular graphics is the discipline and philosophy of studying molecules and their properties through graphical representation. IUPAC limits the definition to representations on a "graphical display device"...
  
  
• Molecular dynamics
  Molecular dynamics
  Molecular dynamics is a computer simulation of physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a period of time, giving a view of the motion of the atoms...
  
  
• Software for molecular mechanics modeling

External links

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