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.

Select File(s)

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.

How does converting PDB to STL work?

In order to successfully convert an PDB formatted file to the STL format, our converter tools will perform several initial checks to ensure the file provided is indeed an PDB file. There are many files out there where the file type extension does not match the data contained within the file. Along with these file type checks, our tools will do additional checks to ensure the file is correctly formatted to match the provided file type. There are many tools out there that do not always create PDB files to the exact specification.

Take your PDB file

An PDB file is a binary data file containing 3D data that makes up the 3D model, including vertices, faces, texture coordinates, and more. To guarantee efficient conversions, our tool will check all data that is contained within the PDB file and remove any information that is duplicated. This not only ensures the conversion completes more quickly, but also the generated STL file size is smaller.

Convert the data from PDB to STL

Now that the data from the PDB file has been processed, our tool can apply any conversion specified options, such as enabling Voxel mode, and with these applied, prepare the data to be converted to the final STL file format. Part of this process ensures checking the capabilities of the STL format and removing any data that cannot be represented.

Save to the STL format

At this point, the PDB to STL conversion tool will have the 3D model in a state that is ready to be transferred to the STL format. Our tool creates the STL file, ensuring all the model data is present and is formatted to match the STL file specification to ensure the file opens in compatible STL file editors. To ensure a compact file size, our PDB to STL converter will always save the STL file in a binary format.

File format information for PDB and STL

Extension	PDB
Full Name	Protein Data Bank
Type	3D Model
Mime Type	application/octet-stream
Format	Binary

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.

Extension	STL
Full Name	Standard Triangle Language
Type	3D Model
Mime Type	application/vnd.ms-pki.stl
Format	Text
Opens With	Blender, 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.