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How to convert PDB (Protein Database) to PLY (Stanford .ply)?

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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.

PLY

PLY can generally be considered a simple, 1990s-era, university research oriented polygonal (mesh) 3D file format designed to store data from 3D scanners. It was developed by Greg Turk and others in the Stanford graphics. Its design was inspired by the Wavefront .obj format.

PLY was meant to be a simple, easily parsable file format and hence only conveys basic geometry information for a single object definition with polygon vertices, vertex colors vertex normals and UV texture coordinates. No materials nor hierarchy, lights or cameras are supported.

PDB import converter's overview

PLY export converter's overview