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UCSF Chimera is a highly extensible, interactive molecular visualization and analysis system. Chimera can read molecular structures and associated data in a large number of formats, display the structures in a variety of representations, and generate high-quality images and animations suitable for publication and presentation. In addition, Chimera provides tools to: show density maps and analyze microscopy data; utilize symmetry information for the display of higher-order structures; display multiple sequence alignments, with crosstalk between the sequences and structures; and enable analysis of molecular dynamics trajectories and docking results.

Chimera is distributed with full documentation and a number of tutorials, and can be downloaded free of charge for academic, government, non-profit, and personal use. Chimera is available for several platforms, including Windows, MacOS X, and Linux. For more information, see the Chimera web site. Chimera is developed and supported by the Resource for Biocomputing, Visualization, and Informatics and is funded by the NIH National Center for Research Resources (grant P41-RR01081).

  Selected Features:

  Molecular Graphics  |   Chemical Knowledge  |   Sequence Viewer  |   Volume Data  |   Multiscale Models  |   Molecular Dynamics  |   Screening Docked Molecules  |   User-Driven Analysis  |   More...  


    All images on this page are Copyright © 2004 by The Regents of the University of California; all rights reserved.
Amino Acid example

Molecular Graphics

  • interactively manipulable stick, ball-and-stick, CPK, ribbon, and special nucleotide representations; molecular surfaces
  • highly intuitive translation, scaling, and rotation; Side View tool for adjusting clipping planes and scaling
  • interactive color editing in various color spaces (RGB, CMYK, etc.), including transparency
  • ability to save high-resolution images for presentation and publication
  • stereo viewing (side-by-side and time-sequential)

Chemical Knowledge

hydrogen bonds
  • determination of atom types in arbitrary molecules, including non-standard residues
  • ability to add hydrogen atoms
  • high-quality hydrogen bond identification
  • selection of atoms/bonds by element, atom type, functional group, amino acid category
  • interactive bond rotation, distance and angle measurements


Sequence Viewer

The Multalign Viewer extension displays multiple sequence alignments, calculates and shows a consensus sequence and conservation histogram, and allows regions to be defined and colored. sequence Structures opened in Chimera are automatically associated with a matching sequence. Structures can be superimposed based on the sequence alignment, and actual/predicted secondary structure features can be depicted on the alignment. When a region is defined by dragging within the sequence, the corresponding residues of the structure are highlighted. The color swatches behind the sequence names match the corresponding structures.

Volume Data

Chimera can display three-dimensional electron and light microscope data, x-ray density maps, electrostatic potential and other volumetric data. Contour surfaces, meshes and volumetric display styles are provided and thresholds can be changed interactively. Maps can be colored, sliced, segmented, and modifications can be saved. Markers can be placed and structures can be traced. The accompanying image shows a density map of Kelp fly virus from electron microscopy colored radially and with an octant cut out.

Volume Data

Multiscale Models

Multiscale Models

The Multiscale extension allows Chimera to display large complexes such as virus capsids, ribosomes, and chromatin. It displays quaternary structure of PDB models and allows you to select subunits and show atomic resolution detail. Matrices are read from PDB files that specify the biological unit. Crystallographic packing can also be shown.

Molecular Dynamics / Lenses

Chimera can display molecular dynamics trajectories in a variety of formats: AMBER, CHARMM, GROMACS, GROMOS, MMTK, NAMD, PDB, and X-PLOR. All normal Chimera analysis and display capabilities are available with trajectories. One such capability is to place "lenses" on the screen: rectangular regions containing markedly different display properties. The accompanying image shows one trajectory frame of a buckytube immersed in water. A lens has been placed over the center of the buckytube to reveal the hydrogen-bonded chain of waters in the center of the tube, along with their residue numbers. The simulation was done with polarizable molecular dynamics using the Amber8 Sander module, and provided courtesy of J. Caldwell.

bucky tube with waters

View Dock image

Screening Docked Molecules

The program DOCK calculates possible binding orientations, given the structures of "ligand" and "receptor" molecules. Typically, a large database of small molecule structures is searched for compounds that may bind the receptor. The Chimera extension ViewDock facilitates interactive selection of promising compounds from the output of DOCK. The molecules can be viewed in the context of the binding site and optionally, screened by number of hydrogen bonds to the receptor. The Dock Prep extension prepares a receptor for input to a docking program by adding hydrogens, assigning partial charges, and performing other related tasks.

User-Driven Analysis

Users can easily import structure-related data into Chimera in the form of "attributes," i.e. values associated with atoms, residues, or models. The data can be imported with the Define Attribute extension and then visually represented as color ranges, varying atom sizes, or "worm" backbone depictions, using the Render by Attribute extension. Such data can also be manipulated programmatically in Chimera, and in fact Chimera was designed with extensibility and programmability in mind. It is largely implemented in Python, with certain features coded in C++ for efficiency. Python is an easy-to-learn interpreted language with object-oriented features. All of Chimera's functionality is accessible through Python and users can implement their own algorithms and extensions without any Chimera code changes, so any such custom extensions will continue to work across Chimera releases. Many programming examples are provided to assist extension writers.

User-Driven Analysis

More Details

For more details on these and other Chimera capabilities, please see our examples page.

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