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| Chimera (software) | |
|---|---|
| Name | Chimera |
| Developer | University of California, San Francisco |
| Released | 2000 |
| Programming language | C++, Python |
| Operating system | Linux, macOS, Windows |
| Genre | Molecular modeling, visualization |
| License | Academic freeware |
Chimera (software) is a molecular visualization and analysis application developed for structural biology, computational chemistry, and bioinformatics. It integrates tools for macromolecular modeling, density map interpretation, and sequence-structure analysis to support research in structural biology, crystallography, and cryo-electron microscopy. Chimera has been developed at the University of California, San Francisco and is widely used alongside tools from institutions such as the European Molecular Biology Laboratory and the Howard Hughes Medical Institute.
Chimera originated in the late 1990s at the University of California, San Francisco under projects associated with the Resource for Biocomputing, Visualization, and Informatics and released its first versions in 2000. Early development was influenced by visualization efforts at the Molecular Graphics Lab, RCSB PDB and collaborations with researchers from Stanford University, Massachusetts Institute of Technology, and the National Institutes of Health. Over successive releases Chimera incorporated algorithms from groups at the Lawrence Berkeley National Laboratory and integrated map-fitting techniques developed in labs linked to the European Bioinformatics Institute and the Max Planck Society. Funding and contributions have come from agencies including the National Science Foundation and the National Institute of General Medical Sciences. Chimera's evolution paralleled advances in techniques pioneered at the European Molecular Biology Laboratory and the Janelia Research Campus for cryo-EM reconstruction and model building.
Chimera combines a graphical user interface with a modular architecture that supports visualization, measurement, and modeling workflows used by scientists from the Protein Data Bank, Cold Spring Harbor Laboratory, and diverse research groups at the University of Cambridge. Core features include interactive rendering of macromolecules, surface generation, electrostatics display using implementations related to work from the San Diego Supercomputer Center, and animation export utilized by teams at the Scripps Research Institute. Architectural components parallel designs found in software from the National Center for Biotechnology Information and employ rendering pipelines influenced by graphics research at the California Institute of Technology and the University of Illinois Urbana–Champaign. Chimera's interface integrates menu-driven controls with command-line scripting similar to systems used at the European Molecular Biology Laboratory-European Bioinformatics Institute.
Chimera is distributed for major desktop platforms including Linux, macOS, and Microsoft Windows. Binary builds and source distributions have been adopted in computational environments at institutions such as the Argonne National Laboratory, Oak Ridge National Laboratory, and the Swiss Federal Institute of Technology in Zurich. Compatibility layers and packaging practices mirror approaches used by projects at the Debian Project, Red Hat, and the Homebrew community, while integration with cluster resources follows conventions from the XSEDE network and the European Grid Infrastructure.
Chimera reads and writes widely used structural biology formats such as those from the Protein Data Bank, map formats from cryo-EM pipelines developed at the European Molecular Biology Laboratory, and coordinate formats used in crystallography at the International Union of Crystallography. It supports density formats compatible with software from the Automated Molecular Microscopy and import/export workflows that interoperate with tools from the UCSF Structural Biology community. File handling routines follow conventions similar to parsers used by the Biopython project and exchange formats used by the CCP4 suite and the Phenix project.
Chimera provides an extensions mechanism and a Python-based scripting interface adopted by developers from the Open Science Grid, European Bioinformatics Institute, and many university laboratories including Harvard University and Yale University. The plugin architecture has enabled community contributions for tasks developed alongside toolchains from the Rosetta Commons and the AutoDock community. Scripting capabilities allow interoperability with workflow managers and pipeline systems used at the Broad Institute and integration with visualization workflows pioneered at the Visual Molecular Dynamics group.
Chimera is optimized for interactive performance on desktop workstations and leverages parallelization concepts used at the National Center for Supercomputing Applications for handling large assemblies. Typical use cases include model building for projects at the European Molecular Biology Laboratory, map interpretation in cryo-EM workflows used by researchers at the National Center for CryoEM Access and molecular presentation preparation for journals affiliated with the American Society for Biochemistry and Molecular Biology. It has been employed in structural studies conducted at the Max Planck Institute and in educational settings at institutions such as the University of Oxford.
Chimera is frequently compared with visualization tools developed by the University of Illinois, the Scripps Research Institute and commercial platforms used in industry at companies like Schrödinger. Reviews in community forums and methods papers reference comparisons with packages from the Molecular Graphics Lab, RCSB PDB, PyMOL, and VMD with respect to scripting, rendering quality, and extensibility. Academic adoption at centers including the European Molecular Biology Laboratory and the RCSB Protein Data Bank reflects its standing among open academic tools favored alongside platforms from the Phenix and CCP4 ecosystems.
Category:Molecular graphics programs