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PDB to Universal Scene Description
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How to convert PDB (Protein Database) to Universal Scene Description (.usd,.usda, .usdc.usdz)?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. |
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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. |
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Universal Scene Description The USD format (“Universal Scene Description”) is an open 3D model and scene format designed for efficient storage and streaming of 3D asset data. It is a high-performance extensible framework and ecosystem for describing, composing, simulating, and collaboratively navigating and constructing 3D scenes. An extensive overview of USD is provided in the Okino USD documentation. Pixar Animation Studios originally created the USD platform (as its fourth generation variation after its Marionette & Preso systems) to improve studio-wide collaborative workflows. USD provides a concept of "scene composition", building a unified scene from potentially thousands of loosely-coupled source assets. For example, the mesh, rigging, materials, and animation for a single model might all come from different "layers" (files), each created and maintained by a different artist or department. Layers can store multiple "variants" of any given data, helping to solve problems of versioning/approval. The coupling between layers is very dynamic and loose, allowing for greater flexibility during the production process. The entire USD system is designed to facilitate a large studio making feature films, with all of the scale that that implies. USD should be considered more of a code framework (“OpenUSD”) for use in group collaboration, to help with the aggregation of various 3D data sources into a unified scene through a process referred to as scene composition. A subset of that code framework provides for reading and writing USD disk-based files as well as rendering USD scenes (Hydra). The system is rather complex to implement (for software developers) and to use (from first principles) as a 3D graphics artist. The USD file format itself is not for faint of heart and is best read/written using the OpenUSD SDK + various programming APIs. More commonly used ASCII 3D file formats such as COLLADA, VRML2 and Wavefront OBJ are much easier to manipulate/understand/use on a human level basis. File extensions used by the standard include:
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