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How to convert PDB (Protein Database) to 3MF?

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.

3MF

3MF, 3D Manufacturing Format, is a modern replacement for the legacy STL (StereoLithography) file format with an explicit focus on the proper transmission of CAD and non-CAD model data for 3D printing as well as to downstream services and platforms. From Okino's long term perspective, the VRML2 file format was and is "just as good" for such requirements but never had the correct understanding nor traction since its introduction in 1995.

Features of 3MF over the legacy STL format includes: geometry instancing support, layered texture maps, multiple layers of UV texture coordinates, vertex colors and extended material types.

History, features, overviews, implementation partners and more can be read on the 3MF Consortium’s web site.

Note: Microsoft Windows uses the 3D Manufacturing Format (.3mf) for all 3D printing tasks.

Please also refer to the 3MF export converter for more information related to 3MF.

PDB import converter's overview

3MF export converter's overview