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Home > Supported File Formats > PDB to U3D


How to convert PDB (Protein Database) to U3D (Universal 3D, 3D PDF)?


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.

     

U3D

U3D is a semi-obsolete 3D mesh file formats from the 2000-2009 era of the 3D graphics world and whose history is little understood outside the confines of a few 3D graphics companies. Even so, U3D is still a fine 3D file format as a pipeline to get 3D data embedded within 3D PDF files, especially with the full and extensive implementation made by Okino.

For more details on the U3D file format, its core features and limitations, how to embed U3D files within 3D PDF files and the features of the Okino U3D import/export converters, please refer to this WEB page.

Generally speaking, U3D was implemented by a few 3D companies in the mid to late 2000s when it was pushed by Adobe+Intel as part of the line of 'Acrobat-3D' software packages. In very loose terms, U3D is used to convey and embed 3D model data within 3D PDF files, where PDF would be the container for the 3D data.

U3D started off in the 1990s as Intel's "IFX" gaming toolkit which was than thrust upon Macromedia, Alias Research, Softimage and other similar companies around the year 2000 to be accepted as a new "industry standard" 3D file format called "Shockwave-3D". The dotCOM bubble caused SW-3D to die pre-maturely after 2001 only to be rebranded as U3D or the "Universal 3D file Format" in 2004 (ECMA-363). Its specification PDF document described it as "An extensible format for downstream 3D CAD repurposing and visualization". However, U3D was highly profit/sales motivated/biased and not consumer/end-user motivated. As such, partly due to the 2008/2009 recession, those companies and their investments in U3D died away.

Okino is and was critical of U3D back in the day as it was the company which created the main conversion implementation of U3D for both import and export. It understood the limitations of U3D well and of its false promotion as a "universal file format" whose title should really have gone to those such as COLLADA, FBX, VRML2, etc. When implemented well U3D is a fine file format by itself but few companies invested enough time and money to support U3D import and export in a most ideal manner.