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How to convert PDB (Protein Database) to VRML (VRML2, VRML97, X3D)?

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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.

VRML

VRML2 ("Virtual Reality Markup Language") is one of the very best of non-MCAD file formats, little appreciated and lost (mainly) to the annals of time. Many people (wrongly) believe that FBX is the primary "translation file format" but VRML2 pre-dated it by at least 10+ years and has equally good or better functionality (and in an open, non-proprietary specification). It was supplemented or augmented by the X3D (XML-based) file format in the mid 2000s. The Web3D Consortium supports the evolution of VRML2/X3D and of its acceptance as ISO and IEC standards.

Without getting into specifics, VRML2 can be considered a "rich file format" in terms of its functionality and capabilities, yet few software programs fully utilize all of that functionality. It could have, and should have, become the defacto "universal 3D file format" for data translation and long term storage but it did not have the clout nor marketing dollars that other newer formats had such as from Autodesk (FBX, DWF), Sony (COLLADA), Adobe+Intel (U3D), Dassault Systemes (3DXML) and others.

VRML1 and VRML2 are 3D file formats with a long and complex history. They were originally developed in the mid 1990s to define 'interactive 3D worlds' on the then-new World Wide WEB. However, statistically speaking, VRML2 became more well known as a high quality "data translaton and storage" file format, partly due to Okino pushing it as such a standard in the industry. It was implemented by a good number of 3D software packages and hence became a "reliable back door" to convert 3D assets out of those packages before FBX, DWF, COLLADA, U3D and other similar file formats came along in the mid to late 2000s, or glTF in the late 2010's.

It is also known as VRML2, X3D, Classic VRML, VRML97, VRML1 and Inventor2.

PDB import converter's overview

VRML export converter's overview