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How to convert PDB (Protein Database) to PLM XML (Siemens)?

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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.

PLM XML

PLM XML is a format created by UGS for facilitating product lifecycle interoperability using XML. Representing a variety of product data both explicitly and via references, PLM XML provides a lightweight, flexible mechanism for transporting high-content product data over the internet.

Related to PLM XML, Okino was one of the very first members of the Siemens 'JT Open' initiative and hence we provide excellent support for the import and export of JT files. "JT" is the predominant and lightweight 3D visualization file format for PLM. Due to the overlap in functionality between JT files and PLM XML files, we do support PLM XML directly but rather we rely upon JT for our PLM coverage.

PDB import converter's overview

Vist the Siemens WEB site

JT export converter's overview