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| Rasmol | |
|---|---|
| Name | Rasmol |
| Caption | Molecular visualization in Rasmol |
| Developer | Roger Sayle |
| Released | 1992 |
| Latest release | varies (legacy) |
| Operating system | Cross-platform |
| Genre | Molecular graphics |
| License | Proprietary / open-source variants |
Rasmol is a molecular graphics program for visualizing macromolecular structures such as proteins, nucleic acids, and small molecules. It was originally authored for interactive exploration of three-dimensional coordinates from crystallography, NMR, and computational modeling, and has been widely used in structural biology, chemistry, and bioinformatics communities. The program's lightweight design and scriptable command language enabled integration into educational, research, and publishing workflows.
Rasmol was created in 1992 by Roger Sayle following advances in computational crystallography and the needs of researchers using data from the Protein Data Bank, Brookhaven National Laboratory, European Molecular Biology Laboratory, and laboratories influenced by figures such as Richard Dickerson, Ada Yonath, John Kendrew, Max Perutz, and Linus Pauling. Its emergence paralleled software developments like Molecular Graphics Laboratory tools, O/MSMS, Grasp, PyMOL, and Swiss-PdbViewer in the 1990s, responding to datasets from X-ray crystallography, Nuclear magnetic resonance, and early molecular dynamics simulations influenced by groups at Brookhaven, European Bioinformatics Institute, Cambridge University, MIT, and Stanford University. Over the 1990s and 2000s, Rasmol influenced visualization in projects associated with institutions such as National Institutes of Health, Wellcome Trust, Howard Hughes Medical Institute, and the European Molecular Biology Organization.
Rasmol provides interactive 3D rendering with representations including wireframe, stick, ball-and-stick, space-filling (CPK), backbone ribbon, and cartoon-style traces used by researchers at Harvard University, University of Cambridge, California Institute of Technology, Yale University, and University of Oxford. It supports coloring schemes by atom type, chain, residue, and secondary structure, facilitating comparison with depictions in publications by authors like Jane Richardson, Michael Levitt, Martin Karplus, and Kurt Wüthrich. The command-line scripting language enables automated figure generation akin to scripting in PyMOL, VMD, UCSF Chimera, and ChimeraX, and has been used in workflows linking to tools from NCBI, EMBL-EBI, RCSB PDB, and academic packages developed at Scripps Research, Max Planck Institute, and Lawrence Berkeley National Laboratory.
Rasmol reads common structural coordinate formats such as PDB and mmCIF, formats produced by experimental facilities like Diamond Light Source, APS (Argonne), and ESRF, and supports ancillary formats for trajectories and electron density via converters used by software from Daresbury Laboratory and groups collaborating with European Synchrotron Radiation Facility. It interoperates with visualization and analysis pipelines involving CNS, XPLOR, GROMACS, AMBER, CHARMM, and file exchange systems maintained by RCSB PDB, PDBe, and PDBj. Export capabilities include raster and vector artwork compatible with publication workflows at journals like Nature, Science, Cell, Journal of Molecular Biology, and Proceedings of the National Academy of Sciences.
Originally distributed with source and binaries by its author, Rasmol's distribution history includes shifts between permissive availability and proprietary variants, with derivative projects taking different licensing approaches mirrored by projects such as PyMOL (open-source and commercial editions), Jmol (open-source, Java-based), and utilities maintained by community groups at SourceForge and GitHub. Development activity overlapped with contributions from academic developers at University of California, San Francisco, University of Washington, University of Tokyo, Imperial College London, and volunteer maintainers inspired by initiatives from Open Bioinformatics Foundation and collaborative efforts at EBI.
Rasmol has been used in education for teaching structural concepts in courses at Massachusetts Institute of Technology, University of California, Berkeley, Imperial College, and University of Edinburgh, and in research settings for rapid inspection of coordinates generated by facilities like Diamond Light Source and Brookhaven National Laboratory. Practical applications include preparation of figures for publications in venues such as Nature Structural & Molecular Biology, structural validation in projects coordinated with RCSB PDB and PDBe, and integration into pedagogical resources used by museums and outreach programs associated with Smithsonian Institution and American Chemical Society. Its lightweight nature made it suitable for inclusion in web-based tutorials linked from portals run by NCBI, EMBL-EBI, and undergraduate curricula at universities including Princeton University and University of Chicago.
Rasmol received acclaim in the 1990s and early 2000s for democratizing access to molecular visualization, influencing the development of successors like Jmol, PyMOL, VMD, and Chimera. Reviews in educational and computational chemistry contexts compared it with contemporaries developed at institutions such as Scripps Research Institute, Los Alamos National Laboratory, and Brookhaven National Laboratory, noting its speed and scriptability. It is cited in historical accounts of structural bioinformatics alongside developments at Protein Data Bank, European Bioinformatics Institute, RCSB PDB, and software efforts associated with NIH funding, and remains referenced in retrospectives by structural biologists such as Jane Richardson and computational chemists like Martin Karplus.
Category:Molecular graphics software