Convert PDB to OBJ (Free)
Also converts STL, GLB, PLY, USDZ, 3MF, FBX from the same file.
Runs in your browser. No upload, no signup, nothing to install.
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How to convert PDB to OBJ
- 1
Open your .pdb file
Drag it onto the viewer above, or click "Open a PDB File". Files up to 200 MB open directly; the parse runs in a worker so the page stays responsive.
- 2
Click Download OBJ
Once the file is open, the Download OBJ button sits at the bottom right of the viewer. The Export menu in the toolbar has every other format.
- 3
Download
The .obj 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 PDB into OBJ, and what does not.
| Geometry | Kept | Both formats store triangle meshes, so the shape transfers directly. |
|---|---|---|
| Colors and materials | Kept | OBJ carries material colors, which is at least what PDB stores, so the colors come across. |
| Layers and structure | Kept | Layers survive as real layers in the OBJ file, so you can still isolate and toggle them. |
| Units and scale | Reduced | PDB 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 OBJ writer emits: OBJ plus a companion MTL, zipped together. Each layer becomes an object block and each mesh a named group with its material color. Lines are written as OBJ line elements and point clouds as point elements.
The source: Protein Data Bank structure (PDB) (.pdb, .ent, .pdbqt, .pqr)
A Protein Data Bank structure (also PDBQT from AutoDock and PQR from APBS) in ångströms: proteins as a cartoon of their chains with helices and strands, DNA and RNA as a backbone tube with base sticks, ligands as ball and stick, every atom coloured by element, with polymer atoms, hydrogens, water and space filling on layers of their own. The first model of the file is read.
The target: Wavefront OBJ (.obj)
The lowest common denominator of 3-D interchange. Practically every 3-D application reads it.
Opens in: 3ds Max, Maya, Rhino, Cinema 4D, Blender, MeshLab.
Your file never leaves your computer
Both the PDB parser and the OBJ 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 PDB to OBJ converter free?
Yes. No signup, no watermark, no per-file limit and no paid tier. Innerscene.
▶Is my PDB 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 OBJ export?
OBJ carries material colors, which is at least what PDB stores, so the colors come across.
▶Do layers and named parts carry into the OBJ file?
Layers survive as real layers in the OBJ file, so you can still isolate and toggle them.
▶Will the OBJ open at the right size?
PDB 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 a PDB 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 OBJ back to PDB?
Not here. We read PDB and write OBJ, 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 PDB to something else
Convert something else to OBJ
Or start from the universal 3D viewer.