Home > Supported File Formats > PDB to COLLADA

How to convert PDB (Protein Database) to COLLADA (.dae)?

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.

COLLADA

COLLADA (DAE) is a XML-based readable file format of the 2007/2008 era which had an original goal of allowing efficient cross conversion of 3D asset data between all of the major 3D DCC/Animation systems of that era. Many 3D software programs came to implement COLLADA but with varying levels of comformity and data reliability. COLLADA is more generally known as a polygonal mesh file format and not a MCAD/CAD/AEC/GIS format. Today people would usually use FBX over COLLADA, depending on the quality of the associated (and dated?) import/export converters.

Okino created one of the key implementations of the COLLADA file format in its import and export converters. However, it saw little need for them except for exporting into Cinema-4D from 2008 to 2012, as the primary gateway into Google Earth, and as our still-preferred method to move 3D assets into Blender (rather than FBX). COLLADA does have its place in these current and prior times.

Okino has a unique take on the COLLADA file format as Okino was at the very center of the DCC/Animation conversion world. In 2007 Rémi Arnaud and Mark Barnes argued that yet-another 3D file format was required and hence Sony funded their efforts to define COLLADA for the cross conversion of assets between (initially) 3ds Max and Maya. However, what they conveniently ignored was that Okino already had the defacto cross conversion system in place, for the prior decade, based on its BDF (binary data translation file format) for 3ds Max, Maya, Cinema-4D, Softimage, LightWave and others. In the mid 2000's there was a "not invented here" mindset and hence everyone wanted to stamp/force their own 3D file format on the industry: FBX (Autodesk), COLLADA (Sony), 3dxml (Dassault Systems), XAML-3D (Microsoft), U3D (Adobe and Intel), etc. There was little need or reason to have "yet-another" set of new 3D file formats. All, except FBX, would basically come and go as of 2007/2008. The implosion of the DCC/Animation industry of 2005-2007 and the 2008/2009 recession further hampered the long term adoption or need for COLLADA over Autodesk's FBX.

COLLADA is/was a very fine file format but it was really not needed at the time of its introduction in 2007. It only introduced yet-more confusion to the 3D graphics market as to which 3D file format to use to transfer 3D assets between packages. Developers generally implemented v1.4 of the COLLADA file specification then lost interest thereafter.

However, as a saving grace for COLLADA, all of the 3D software packages which had implemented a good COLLADA exporter became instant gateways to move their 3D assets into the then-new glTF file format of the mid 2010s, until such time that these same packages could add in their own glTF exporters.

PDB import converter's overview

COLLADA export converter's overview