Convert MOL2 to PLY (Free)
Also converts STL, OBJ, GLB, USDZ, 3MF, FBX from the same file.
Runs in your browser. No upload, no signup, nothing to install.
Also from Innerscene: Circadian Lab, a free lighting calculator for room illuminance, melanopic EML, and glare.
How to convert MOL2 to PLY
- 1
Open your .mol2 file
Drag it onto the viewer above, or click "Open an MOL2 File". Files up to 200 MB open directly; the parse runs in a worker so the page stays responsive.
- 2
Click Download PLY
Once the file is open, the Download PLY button sits at the bottom right of the viewer. The Export menu in the toolbar has every other format.
- 3
Download
The .ply is written in the browser and saved straight to your downloads folder. No queue, no email, no watermark.
What survives the conversion
A file conversion is a translation, and formats do not carry the same things. Here is exactly what moves from MOL2 into PLY, and what does not.
| Geometry | Kept | Both formats store triangle meshes, so the shape transfers directly. |
|---|---|---|
| Colors and materials | Kept | PLY carries per-vertex color, which is at least what MOL2 stores, so the colors come across. |
| Layers and structure | Dropped | PLY is a single flat body with no layers or named parts. Everything merges into one object. If you need the structure, export to GLB, OBJ, DXF instead. |
| Units and scale | Reduced | MOL2 coordinates are in ångströms, and the export treats one ångström as one meter: a protein 50 Å across arrives 50 meters across. Scale the model on import to the size you want. |
What the PLY writer emits: Binary little-endian PLY with x/y/z and per-vertex RGB, faces for meshes, edges for linework, vertices only for clouds.
The source: Tripos MOL2 (.mol2, .ml2)
A Tripos MOL2 file in ångströms: each molecule as ball and stick, elements from the SYBYL atom types and bond orders from the bond types, every atom coloured by element, a space-filling layer, and one layer per molecule of a multi-molecule file.
The target: Polygon File Format (.ply)
The scanning and photogrammetry format, and the one interchange format that treats point clouds as first-class.
Opens in: CloudCompare, MeshLab, Blender, Metashape, RealityCapture.
Your file never leaves your computer
Both the MOL2 parser and the PLY writer are JavaScript and WebAssembly running in your own browser tab. There is no upload step, no server-side conversion queue, and no copy of your file anywhere but your machine. That matters for drawings under NDA, for client work, and for anything you would not email to a stranger.
Free to Use, No Signup
There are no accounts and no watermarks on this converter. If it saved you time, the one thing we ask is a mention: a post, a link from your blog or course page, or a reply to someone asking how to open a file.
Share it
Made something reusable? Add it to the Free Parts Library. Writing about it? Copy a link, badge or citation. Send us your post and we’ll feature it with a link to your site.
Hear about new formats
Occasional emails when the viewer learns a new format or gets a new tool.
Frequently asked questions
▶Is this MOL2 to PLY converter free?
Yes. No signup, no watermark, no per-file limit and no paid tier. Innerscene.
▶Is my MOL2 file uploaded anywhere?
No. The file is read with the browser file API and converted in the same tab. Nothing is sent to a server unless you explicitly click Share, which is a separate, opt-in feature.
▶Will my colors and materials survive the PLY export?
PLY carries per-vertex color, which is at least what MOL2 stores, so the colors come across.
▶Do layers and named parts carry into the PLY file?
PLY is a single flat body with no layers or named parts. Everything merges into one object. If you need the structure, export to GLB, OBJ, DXF instead.
▶Will the PLY open at the right size?
MOL2 coordinates are in ångströms, and the export treats one ångström as one meter: a protein 50 Å across arrives 50 meters across. Scale the model on import to the size you want.
▶How large an MOL2 file can I convert?
Up to 200 MB, and the ceiling adapts to how much memory your device reports. The conversion runs on your own hardware, so a desktop with plenty of RAM will handle more than a phone.
▶Can I convert PLY back to MOL2?
Not here. We read MOL2 and write PLY, but not the reverse. the universal 3D viewer
▶Which browsers does it work in?
Chrome, Edge, Firefox and Safari, on Windows, macOS, Linux, iOS and Android. No plugin and no extension.
Convert MOL2 to something else
Convert something else to PLY
Or start from the universal 3D viewer.