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How to convert PDB (Protein Database) to glTF?

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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.

glTF

As described more extensively on Okino's dedicated glTF converter page, glTF is a newer 3D file format designed for the "last mile" of efficient, real-time delivery of 3D assets for Web-based browsers, AR/VR applications and gaming applications, amongst others. It is generally not to be considered as a long term and high fidelity 3D data storage format (such as FBX, COLLADA or VRML2) but rather an efficient transmission and viewing 3D file format. It has begun to gain good traction in recent years.

glTF stands for Graphics Language Transmission Format. glTF is intended as a vendor-neutral distribution format for 3D content, bridging the gap between 3D content creation tools and applications displaying 3D graphics. It is fully graphics API and operating system-independent.

Okino has one of the most extensively developed and refined implementations of glTF for both import and export.

PDB import converter's overview

glTF export converter's overview