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How to convert PDB (Protein Database) to STL (StereoLithography)?

PolyTrans|CAD+DCC performs mathematically precise CAD, DCC/Animation, GIS and BIM 3D file conversions into all key downstream 3D packages and file formats. Okino software is used and trusted throughout the world by many tens of thousands of 3D professionals in mission & production critical environments, backed by respectable personal support directly from our core development team.

PDB

If you are coming here looking for information about the Microsoft .pdb file format then this is the wrong place. Those .pdb files define a 'program database file' that contains debugging information for a compiled executable (EXE/DLL). PDB files are generated by Microsoft Compilers when an application program is compiled in debug mode.

Rather, this page describes the 'Protein Database' 3D file format which uses the .pdb file extension.

The Protein Databank (PDB) is an archive of experimentally determined three-dimensional structures of biological macromolecules, serving a global community of researchers, educators, and students. The archives contain atomic coordinates, bibliographic citations, primary and secondary structure information, as well as crystallographic structure factors and NMR experimental data.

The database is constantly updated as new structures are deposited by the international scientific community. As described on a PDB database WEB page, most of the three-dimensional macromolecular structure data in the Protein Data Bank were obtained by one of three methods: X-ray crystallography (over 80%), solution nuclear magnetic resonance (NMR) (about 16%) or theoretical modeling (2%).

The PDB file format is a text-based file format that is designed to convey information about the structure of molecules; namely organic compounds such as proteins. This information consists of atomic co-ordinates, element composition, chain and grouping characteristics and bonding information.

STL

STL (StereoLithography) is one of the industry's oldest (and simplest) 3D file formats created back in 1987 for 3D Systems' first commercial 3D printer. It is widely used for rapid prototyping, 3D printing and CAM. Okino has provided one of the very first and still primary STL export conversion systems for close to 3 decades.

Please take note that there is no 3D file format which is much simpler than STL. It is not a high-end, high fidelity 3D conversion file format as many people have come to wrongly believe. Rather, STL defines just a raw triangulated polygon mesh with no smoothing information (vertex normals), no uv texture coordinates, no assembly hierarchy part naming or any material assignments. 3MF and VRML2 are often much better file formats for moving 3D datasets into downstream programs and/or 3D printers.

The Okino STL exporter WEB page provides good graphical tutorial about how to convert CAD file data into STL and also how to clean a 3D model which is 'almost water tight'.

PDB import converter's overview

How to Convert CAD to STL

STL export converter's overview