Free Online PDB to STL Converter

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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.

How to Convert your PDB to STL Online?

Here are 2 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.

File format information for PDB and STL

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

A PDB (Protein Data Bank) file is a standard file format used to store information about the three-dimensional structure of biological molecules, particularly proteins and nucleic acids. It contains detailed atomic coordinates, information about the chemical structure of the molecules, and metadata such as the experimental methods used to determine the structure. The PDB format is crucial in the field of structural biology, providing a standardized way to share and disseminate structural data. Researchers can use PDB files to visualize and analyze the spatial arrangement of atoms in a molecule, aiding in understanding its function and interactions with other molecules.

PDB files are typically generated through experimental techniques like X-ray crystallography, nuclear magnetic resonance (NMR), or electron microscopy. Each atom in the molecule is represented by its coordinates in three-dimensional space, and additional information such as atom types, bond lengths, and angles is included. This wealth of data allows scientists to create accurate visualizations of molecular structures, supporting various applications in drug discovery, biomolecular engineering, and understanding the fundamental processes of life at the molecular level. The PDB is a global repository, and its files are freely accessible, fostering collaboration and accelerating progress in structural biology.

In addition to atomic coordinates, a PDB file may also contain information about the experimental conditions, references to relevant scientific literature, and annotations that describe specific features of the molecule. Various software tools and databases support the retrieval, visualization, and analysis of PDB files, making them a fundamental resource for researchers across diverse scientific disciplines. The format has evolved over time to accommodate the growing complexity of structural data, and it continues to play a pivotal role in advancing our understanding of the intricate structures that underlie the functions of biological macromolecules.

PDB Converter Capabilities

When converting 3D Model/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 modelling 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 flavours: 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/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 too.

Frequently Asked Questions

How can I convert my PDB file to STL?

First click the "Upload..." button, 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 straight 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.