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Home > Supported File Formats > PDB to FBX


How to convert PDB (Protein Database) to FBX (FilmBox v5/v6/v7,.fbx)?


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.

     

FBX

FBX is a 3D 'digital asset interchange' file format that had been pushed on the 3D industry by Autodesk after they acquired it from the bankruptcy assets of its prior owners, Alias Research and Kaydara of Canada. FBX has its placed in the DCC/Animation world but it does have its limitations, given that it is a closed and proprietary file format of Autodesk.

Note: if you are one of the many people who use FBX to convert data out of Navisworks, Revit, AutoCAD or Inventor then please use DWF-3D file format and Okino's DWF-3D import converter instead. It is a night and day difference but little known except to our core Okino users. Likewise, use our native program support for 3ds Max, Maya and Cinema-4D rather than use FBX.

FBX supports all the common attributes of a DCC/Animation file format such as mesh geometry with vertex normals and vertex colors, non-solids NURBS ('old school NURBS'), lights, cameras, hierarchy, bones and mesh skinning (deformations), materials and textures. In basic terms, it is similar to the capabilities of the COLLADA and VRML2/X3D file formats, and to Okino's long standard BDF data translation file format.

Okino has a very long history associated with FBX as it created the very first and fully implemented set of FBX import and export converters in 2002, with full animation, skinning and trimmed NURBS support. This was long before anyone had much heard of FBX. And to this very day we are still the only company that actively ships and supports FBX v5 (Kaydara), v6 (Alias) and v7 (Autodesk). However, FBX was just one of many 'not invented here' file formats which came to glut the 3D market in the 2005-2007 era, many of which petered away over time.

A key reason for its early adoption, throughout the 3D industry, was the availability of a free and officially supported (but closed) FBX SDK from Autodesk.

The downsides of the FBX file format is that (1) it has stagnated in recent years, (2) it is based on a legacy material model and not on modern PBR, (3) it is based on legacy lighting models and not on physically based lighting, and (4) it is a closed file format which only Autodesk can update or change. Otherwise, these restrictions have made it easier for software developers to implement FBX just once and then not have to worry about costly yearly revisions.