Free Online PDB to STL Converter

You can use our PDB to STL conversion tool to quickly and easily convert your 3D model files for free. You may upload up to 20 files at one time, and our batch PDB to STL converter will process each 3D model and present you with a download link for each file once completed.

Or drag and drop your files here to upload.
A maximum of 20 files can be uploaded at once.

Please note: Your PDB file, once uploaded to our server, will be deleted 15 minutes after upload, so please download your converted PDB file before this time.

Our 3D model PDB to STL tool will load your PDB file and, where supported, attempt to extract all the relevant 3D features, such as geometry, textures, and animations. To access the 3D conversion configuration options, click the button when you have selected your files. The current options support the ability to voxelize your 3D model and more.

How to Convert your PDB to STL Online?

Here are two simple steps to convert your PDB to STL using our fast and free PDB converter tool.

Upload your PDB file

Click the "Upload a PDB File" button, then select a PDB to upload. The maximum file size is 100MB.

Download your STL

Click the download link to receive your STL file.

Frequently Asked Questions

How can I convert my PDB file to STL?

First, click the "Upload..." button and select your PDB file to upload. Your PDB file will be uploaded to our servers. When the PDB to STL conversion has completed, you can download your STL file right away.

How long does it take to convert my PDB to STL?

We aim to process all PDB to STL conversions as quickly as possible; this usually takes around 5 seconds; however, this can be longer for certain files, so please be patient.

How accurate is the PDB to STL conversion?

We aim to provide the best conversion experience. Our tools are under constant review and development, with new features being added every week.

File format information for PDB and STL

Full NameProtein Data Bank
Type3D Model
Mime Typeapplication/octet-stream

A PDB file (Protein Data Bank) is a file format used to store 3D representations of biological molecules, such as proteins, in a simple-to-use plain text file.

The content of the file contains descriptions for each molecule, its 3D atomic coordinates, and other relevant data, along with connection entries. The data is stored as text and is thus easily editable by hand.

PDB files can be opened with specialist 3D viewing software, or you can use our range of PDB file converters to process PDB files into other 3D formats, such as OBJ.

PDB Converter Capabilities

When converting 3D model or mesh files using our PDB converter, we will attempt to convert color materials into a suitable format for use in the converted file.

Full NameStandard Triangle Language
Type3D Model
Mime Typeapplication/
Opens WithBlender, MeshLab, CAD Assistant, DAZ Studio

The STL, or Standard Triangle Language, file format has been around since the '80s and is supported by most modern 3D modeling applications. In particular, the STL format has become something of a standard format within the area of 3D printing, despite the rise of more modern formats such as 3MF.

STL files come in two flavors: binary or text format. The text format is human-readable, making it easy to perform manual edits, but can lead to very large file sizes. As you can imagine, the binary format is much more compact and represents the majority of the STL files you are likely to encounter.

The format itself is very simple; the 3D model is represented by a sequential list of triangles, with each triangle defined with 3 points consisting of their X, Y, and Z positions, along with an additional vector that contains the face normal (the direction the face is pointing). There is an additional attribute block for each triangle; however, this is largely unused and thus unsupported.

STL Converter Capabilities

When converting your PDB to STL, our tool will attempt to accurately convert any color or material information.

Information for converting from PDB to STL

Your PDB file will be converted to a STL file using our unified 3D model and mesh conversion tool. Our PDB 3D tool performs accurate conversions of 3D elements such as vertices, faces, normals, and relevant material information. As both PDB and STL support color material information, our tool will also attempt to convert the color information.

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