RasMol

RasMol is a free, open-source molecular graphics program for viewing proteins, nucleic acids and small molecules in 3D, used mainly in teaching and in quick checks of structure files. In dentistry its role is modest and specific: dental students and biomaterials researchers use it to look at the molecules behind oral tissues and materials, such as collagen, enamel matrix proteins or bacterial enzymes, taken from the Protein Data Bank. It does not open dental scans, X-rays or CBCT. If you came for a RasMol download, the last stable release is 2.7.5.2.

RasMol was written by Roger Sayle in the early 1990s and later maintained by Herbert J. Bernstein through the RasMol and OpenRasMol projects. It is small, fast and scriptable, and it still runs on modest hardware, which is why it survives in classrooms. Development has been quiet for years, so treat it as a stable classic rather than an actively developed tool.

RasMol at a glance

What it does

• Opens PDB, mmCIF/CIF, MDL MOL, Tripos Mol2 and Alchemy, XYZ, CHARMm and MOPAC files.
• Display styles: wireframe, sticks, ball and stick, spacefill (CPK), backbone, strands, ribbons and cartoons.
• Colour schemes by element (CPK), amino acid (“amino” and “shapely”), secondary structure, chain and temperature factor.
• Dot surfaces, hydrogen bonds, disulphide bridges, labels and distance/angle measurements.
• A command language for selecting atoms and residues, usable interactively or from script files.
• Saves images (GIF by default, plus PostScript and other formats) and can write POV-Ray scenes for high-quality rendering.

How dental teams use it

Show a protein structure in a lecture

1. Download the structure file of interest (for example a collagen or amelogenin entry) as PDB from the Protein Data Bank website.
2. Open it in RasMol, choose Display > Cartoons and Colours > Structure to show helices and sheets.
3. Rotate to a clear view and save an image for slides.

Highlight specific residues

1. In the command window type select cys, then spacefill to show cysteines as spheres.
2. Use colour amino to colour residues by type; select all returns to the whole molecule.
3. Save the commands to a script so students can reproduce the view.

Check a material’s structure file

1. Open a small-molecule file (MOL, Mol2 or CIF) of a monomer or additive used in dental materials.
2. Switch to ball and stick and measure bond distances with the pick tools.

Install and first run

• Windows: use the RasWin installer. The last Windows build dates from 2012, so test it on your system before relying on it in class.
• macOS: the available builds are old and Intel-only; they may not run on current macOS. On a modern Mac, Jmol or ChimeraX is the practical choice.
• Linux: build from source or use your distribution’s package if one exists.
• On first run, open a file with File > Open; the command-line window next to the graphics window is where most of the power is.
• Gotcha: very large structures and modern PDB features are handled less well than in current viewers.
• Gotcha: the official sites are sometimes unreachable; the SourceForge “openrasmol” project hosts the files and source.

Limitations

• No dental imaging at all: no DICOM, CBCT, intraoral scans or STL.
• No active development in recent years and no Apple silicon build.
• No molecular surfaces beyond dot surfaces, and dated rendering.
• Its dental relevance is limited to education and biomaterials research.

RasMol vs alternatives

For dental imaging rather than molecules, see 3D Slicer or Weasis.

FAQ

Is RasMol free?

Yes. RasMol is free and open source; binary releases are distributed under the GPL.

What is RasMol used for?

Viewing and exploring 3D structures of proteins, DNA and small molecules, mostly for teaching and quick inspection of PDB files.

Is there RasMol for Windows 10 and 11?

The Windows version is called RasWin. The last build dates from 2012, so test it on your system first; Jmol is a maintained alternative.

Is there RasMol for Mac?

Only old Intel builds exist, and they may not run on current macOS. Jmol or ChimeraX are better options on a modern Mac.

What are the RasMol amino acid colours?

The “amino” scheme colours residues by traditional amino-acid properties, and “shapely” uses a related scheme for residues and nucleic acids. Type colour amino or colour shapely in the command window.

RasMol vs PyMOL?

RasMol is lighter and simpler; PyMOL produces far better images and is actively developed. For publications, PyMOL or ChimeraX is the usual choice.

What is the difference between RasMol and OpenRasMol?

OpenRasMol is the open-source project that hosts ongoing RasMol code and releases; the program itself is still called RasMol.

Is there an alternative to RasMol that runs online?

Yes. JSmol, the JavaScript version of Jmol, runs in a web browser without installation.

Last checked against official sources: 26 September 2026 (developer website: rasmol.org). Versions and licence terms change — confirm on the developer's site before deploying in a clinic.