See also: Web services used by UCSF Chimera, sites that provide Chimera web data, Chimera Python scripts
Experimentally determined protein structures, divided into domains as defined by SCOP (Structural Classification of Proteins).
Database of cancer missense mutations in the context of 3D structures, disease classifications, and patient characteristics. The 3DMol window for viewing associated PDB structures includes an option to download a Chimera session of the structure with mutated positions shown and colored by mutation frequency. The Cancer3D database is described in Sedova et al., Nucleic Acids Res 47:D895 (2019).
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 EMDB.
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.
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.
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.
3DFSC Program Suite
Software for 3D Fourier shell correlation analysis of cryoEM data, available from GitHub. The program requires Anaconda to run, and uses Chimera to display some outputs. See Tan et al., Nat Methods 14(8):793 (2017).
3V: Voss Volume Voxelator
Generates map files of pocket and channel “void” volumes that can be shown as isosurfaces in Chimera; options include a channel finder. The server is described in Voss and Gerstein, Nucleic Acids Res 38:W555 (2010).
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.
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.|
|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 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).
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.
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.
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.
Binding Site Prediction
Kalasanty uses a neural network to predict binding sites in protein structures. The predictions can be saved as .cmap or .cube grid files for display in Chimera or other programs. Kalasanty is described in Stepniewska-Dziubinska et al., Sci Rep 10:5035 (2020) and is available as source code.
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 MOLEonline server runs MOLE, a program for identifying and characterizing channels in macromolecular structures. Results include a profile of the channel radius and hydropathy, a list of residues lining the channel, and scripts for display in Chimera and other programs. The server is described in Pravda et al., Nucleic Acids Res 46:W368 (2018). The image shows results for PDB 1BL8 biological unit calculated in pore mode, displayed in Chimera.
PDBmutator A GUI-enabled script to batch-run Chimera virtual mutation commands (swapna or swapaa) on a PDB file to create all possible structural mutants or all variants defined by a CLUSTAL protein sequence alignment.Partial Order Structure Alignment (POSA) Server
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).
Unifies standard tomogram processing steps in a single python-based toolbox; modified version of Chimera's Volume Viewer available from the PyTom website.
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).
The ScanNet server predicts protein-binding sites for
structures in the PDB, the AlphaFold Database, or uploaded from a local file.
The method is described in
Tubiana et al.,
Nat Methods 19:730 (2022)
and the web server specifically in
Tubiana et al.,
J Mol Biol 434:167758 (2022).
Results are emailed to the user as a zip file containing:
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).