Extract text from 3D model files (MOL)
To convert MOL 3D models to another format, you need ChemDraw or other Data software.
To convert other file formats to the "Chemical Structure Data" file type, you need software like ChemDraw or a similar tool.
The .MOL file format is primarily a chemical table file, specifically an MDL Molfile. These files store the spatial coordinates, atom types, and bond connections for a single chemical molecule. A very small percentage of .MOL files are binary 3D models used in video games like LittleBigPlanet.
Chemoinformatics professionals use specialized software like ChemDraw, ChemAxon Marvin, or ACD/Labs to create, edit, and analyze these files. The format was developed to standardize chemical data exchange, and you can learn more about its technical specifications on the Chemical table file Wikipedia page.
The biggest disadvantage of the .MOL format is its strict limitation to a single molecule per file. If you are managing a library of thousands of compounds, handling individual .MOL files becomes a chaotic and inefficient data management nightmare. Additionally, because the file contains a mathematical matrix of atoms and bonds rather than visual pixels, standard image viewers and web browsers cannot open or display them, forcing users to rely on niche, often expensive software.
To overcome these limits, you should convert .MOL files to SDF (Structure-Data File), which allows thousands of molecules to be bundled into one document. For 3D modeling and structural biology, converting to PDB (Protein Data Bank) or XYZ is recommended. If you just need a visual diagram for a presentation or web page, converting the coordinate data to a 2D image format like SVG or PNG is the best route.
Standard online converters usually fail with .MOL files because they lack the built-in chemical rendering engine required to draw the molecules from raw coordinate text. Often, only specialized chemoinformatics software can accurately export the visual geometry.
Convert.Guru analyzes your MOL file, detects the exact format, and lets you read the text inside.
Users also converted MOL2, CXF, JPG, PNG, CDX, PDF, PDB, CDXML, SDF, JPEG, SKC, MDL and SVG files.
If you want to convert MOL file to PPM, MASS, G, MG, WT, PDB, CSV, JSON, XML, YAML, YML or TOML, you can use ChemDraw or similar software from the "Chemical Structure Data Storage" category. In the File menu, look for Save As… or Export….
To convert DBF, XML, SQLITE, XLSX, SQL, TSV, ACCDB, YAML, MDB, CSV, ODS or JSON files to MOL, try ChemDraw or another comparable tool in the "Chemical Structure Data Storage" category.
The history of Convert.Guru began over 25 years ago in California with Tom Simondi’s file-format database. A former contributor to Space Shuttle development and a software pioneer of the 1980s, Simondi established a trusted resource for file type analysis that was even referenced by Microsoft Windows XP. Today, we use modern technology to process and convert thousands of file formats while continually improving our MOL converter.