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How to convert PDB (Protein Database) to OBJ (Wavefront .obj,.mtl)?

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.

OBJ

Wavefront OBJ is a little understood but highly used and prevalent 3D "polygonal mesh" file format used throughout the 3D graphics world. Okino, Alias Research and McNeel made it popular in the early to mid 1990s as a general purpose, simple-to-read, storage and transmission 3D file format, especially for the then-new companies who began to sell 3D mesh models via the Internet.

Relatively speaking, OBJ is a rather simple file format but a bit better than STL although similar to the more modern 3MF format.The OBJ format allows for 1 or more unique polygonal mesh objects to be defined, each with optional UV texture coordinates and vertex colors. Material definitions can be linked to the mesh geometry as defined in the separate 'MTL' file. The material definitions are rather simple (ie. no PBR material support) but acceptable, and with varied levels of texture mapping support. OBJ format does not provide support for object hierarchy, local transformations, meta data, lights, cameras, skinning or animation. Most notably, OBJ does not allow for 'object instancing' and hence 1000 copies of a screw would be saved to OBJ as 1000 explicit copies, rather than 1000 references to one master object.

A short history: In the 1980s there was a program called Wavefront Visualizer which ran on UNIX and ran its early rendering pipeline as a series of tee'd command line 'applets'. The data flowed from one applet to another via various ASCII based files - OBJ for geometry, MTL for materials and other ASCII files for animation, skinning, deformation, etc.

Okino knows of the Wavefront OBJ file very well as it provides the one and only full implementation of the OBJ file format and with the ability to consume exceedingly large OBJ files quickly and efficiently. This includes the only known implementation of OBJ-centric 'NURBS geometry' (surfaces and curves) within the OBJ file format (which is little or not used) other than that from the McNeel Rhino-3D software.

PDB import converter's overview

OBJ export converter's overview