See also: Web services used by UCSF Chimera, sites that provide Chimera Web data, and Chimera plug-ins on the Web
Experimentally determined protein structures, divided into domains as defined by SCOP (Structural Classification of Proteins).
Database of pre-evaluated conservation and specialization scores for multi-member families of human proteins. Includes downloadable Chimera session files with color-coded structures. Cube-DB is described in Zhang et al., Nucleic Acids Res 40:D490 (2012).
for Aligned Ribosomal Complexes (DARC)
Ribosomal structures from the PDB and EMDB aligned into a common frame of reference. Data processed with Chimera, can be viewed with Chimera. DARC is described in Jarasch et al., Nucleic Acids Res 40:D495 (2012).
Crystallographic electron density maps for Protein Data Bank x-ray structures. Display density maps with Chimera Volume Viewer.
This site contains 3D density maps obtained by electron microscopy in CCP4 format that can be shown with Chimera Volume Viewer.
Presents images, movies, Chimera sessions and details about electron microscopy density maps from the EM DataBank.
A database of human nonsynonymous single-nucleotide polymorphisms (nsSNPs) mapped onto protein structures. Chimera-generated images show SNP locations in the structures and molecular surfaces colored by superfamily sequence conservation and DelPhi-computed electrostatic potential.
A database of three-dimensional protein models calculated by comparative modeling. The website includes links for viewing models in Chimera along with the corresponding template structure and template-target sequence alignment, or colored to show binding site predictions. ModBase models and associated information can also be fetched directly into Chimera.
A database of mouse mutations and phenotypes induced by ENU. Many of the allele pages include molecular structure images and movies made in Chimera (example).
Comprehensive information and tools for the study of protein post-translational modifications; includes scripts for visualization in Chimera.
RCSB Protein Data Bank (PDB),
Protein Data Bank in Europe (PDBe),
Protein Data Bank Japan (PDBj)
Experimentally determined protein and nucleic acid structures. Display PDB and mmCIF format files of atomic coordinates.
Structure-Function Linkage Database
Connecting enzyme structure and function at the level of conserved partial chemical reactions.
UCSC Genome Browser
Chimera links are provided in UCSC Gene pages (see example) and SNP track details pages. Clicking a Chimera link displays the corresponding structure with nonsynonymous SNP residues colored and labeled with the dbSNP identifier.
Atomic resolution virus capsid structures. Some of the capsid images on this site are made with the Chimera Multiscale Models tool.
AlphaSpace is a tool for analyzing surface pockets at protein-protein interfaces. AlphaSpace generates a Chimera session file with several “scenes” for viewing the results in different ways. The program is available upon request from the authors for academic use and is described in Rooklin et al., J Chem Inf Model 55:1585 (2015).
Molecular force field and dynamics simulations. Display trajectories with the Chimera MD Movie extension.
ArbAlign uses the Kuhn-Munkres algorithm to optimally align two arbitrarily ordered isomers, with XYZ input and various options such as whether to consider axis swaps and reflections. The web server uses Chimera to generate WebGL of the results so that the user can rotate and evaluate the fits interactively. The program (which can also be obtained for command-line use) and server are described in Temelso et al., J Chem Inf Model 57:1045 (2017).
Box Beam Backbone Sculptures
Design protein backbone sculptures made from metal box beams or wood. See also Gurnon, Voss-Andreae, and Stanley, PLoS Biol 11:e1001491 (2013). The new user interface was developed by Evan Zelesnik while the old user interface was made by Tom Goddard.
CanDo Atomic Model Generator
|Uses Chimera to generate atomic models of DNA nanostructures from the description in the CanDo (.cndo) file format. Chimera is also used to generate 3D printable models from CanDo.|
|cellPACK is a tool for assembling large-scale models from molecular building blocks; it integrates structural biology and systems biology data with packing algorithms to assemble comprehensive 3D models of cell-scale structures in molecular detail. Chimera can be used to view and analyze cellPACK models.|
|The CoCoPOD platform for Coiled-Coil Protein Origami Design is available on GitHub and described in Ljubetič et al., Nat Biotechnol 35:1094 (2017). Dependencies of the software include Chimera.|
|Given file(s) of predicted contacts, the ConEVA (contact evaluation) server provides several methods for visualizing and comparing them, with or without associated structures. If a structure is available, results include Chimera scripts for 3D visualization. Several example data sets are available on the website. The server is described in Adhikari et al., BMC Bioinformatics 17:517 (2016).|
Given a query structure, the server finds related sequences, aligns them, and displays conservation on the structure. Clicking the link to view results in Chimera uses the Chimera web data mechanism to display the structure and sequence alignment colored by conservation, as well as the ConSurf-calculated phylogenetic tree and custom alignment headers (example).
The server can compare two structures or search the PDB for structures similar to a query. The resulting pairwise superpositions can be viewed in Jmol and downloaded in various forms, including Chimera sessions.
Direct Coupling Analysis
Direct Coupling Analysis (DCA) is a statistical inference framework for identifying direct co-evolutionary couplings among residue pairs in multiple sequence alignments. A protein multiple sequence alignment can be uploaded to the web service, or the code can be downloaded for local use. The download includes a Matlab implementation and scripts for 3D visualization in Chimera as described in Morcos et al., Methods Mol Biol 1137:55 (2014).
Given 3D structures of molecules, DOCK addresses the problem of how they might fit or bind together. Using Chimera, one can:
DROIDS is a pipeline for GPU-accelerated comparative protein dynamics, incorporating graphical user interface control for Amber MD, cpptraj analysis, and statistical and visual representations in R graphics and UCSF Chimera. DROIDS is described in Babbitt et al., Biophys J 114:1009 (2018), and open-source code is available on GitHub.
Dynamo is a software environment for subtomogram averaging of cryo-EM data. As mentioned in the “advanced starters guide,” it can pass maps into Chimera for further visualization and analysis.
Image processing suite for single-particle reconstruction from cryo-EM and working with data from related subdisciplines such as tomography and 2D crystallography. The previous program EMAN1 included the EMANimator extension for making volume-data (map) animations in Chimera.
The EzMol server is a wizard for automated visualization and coloring built on top of 3Dmol.js and UCSF Chimera, developed at Imperial College London.
JEvTrace is a Java implementation of the evolutionary trace method. Results can be shown in Chimera as coloring of the sequence alignment and any associated structures by reading a JEvTrace output file into Multalign Viewer.
The server searches the PDB for matches to a user-specified 3D motif (pattern of residues). The authors provide the Chimera extension ViewMatch for looking through the hits superimposed on the query. LabelHash can also be downloaded for local command-line use.
MMB is a multiresolution modeling tool for building 3D structural and dynamical models of macromolecules, with explicit control over degrees of freedom, forces, and constraints; it was previously known as RNABuilder but now also handles protein and DNA. MMB is available for download along with a plugin for using Chimera as the GUI, as described in Tek et al., Nucleic Acids Res 44:95 (2016).
The POSA server performs flexible multiple structure alignment. The results visualization page includes a link to download a python script for viewing the superimposed structures in Chimera. The POSA server is described in Li et al., Nucleic Acids Res 42:W240 (2014).
PyChimera provides access to the UCSF Chimera codebase from any Python 2.7 interpreter, making it easier to integrate with other software. PyChimera is described in Rodríguez-Guerra Pedregal and Maréchal, Bioinformatics bty021 (2018).
ResMap (Resolution Map) is a Python application for computing the local resolution of cryo-EM density maps. It generates a map of the local resolution and a Chimera script for 3D visualization. ResMap is available on SourceForge and described in Kucukelbir et al., Nature Methods 11:63 (2014). See also: LocalFSC
The Ringer program detects molecular motions by systematically sampling X-ray electron density; the aim is to go beyond static structural snapshots of proteins by uncovering structural ensembles. The program depends on Chimera. Ringer is available for download and is described in Lang et al., Protein Sci 19:1420 (2010).
A tool for molecular modeling and animation that uses Chimera for surface generation.
Assignment of NMR spectra for determining protein and nucleic acid structures. Uses Chimera to display NMR peak assignments on a molecular model.
A Cytoscape app that integrates protein networks or pathways in Cytoscape with visualization and analysis of corresponding structures in Chimera. It also works with RINalyzer to calculate residue interaction networks (RINs) for Cytoscape from protein structures in Chimera.
TALOS is an open-source software package for converting 3D computer-generated design files (PLY) into DNA sequences that can be synthesized and mixed to generate DNA 6HB-based wireframe 3D nanoparticles with high fidelity. TALOS also writes BILD files for display in Chimera.
Given two protein conformations or an ID from the Database of Macromolecular Movements, the server generates a ViewMotions rainbow image and corresponding Chimera session. The conformational change is shown as a series of interpolated structures with variable regions rainbow-colored from blue to red. The server is described in Cockrell and Kantrowitz, J Mol Graph Model 40:48 (2013).
Computational Chemistry List (ccl.net)
PDB Discussion Forum (firstname.lastname@example.org)