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How to convert PDB (Protein Database) to XGL (ZGL)?

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.

XGL

XGL/ZGL is a legacy 3D polygonal mesh file format that had been created by the RealityWave company in the late 1990s. AVEVA purchased RealityWave and integrated the file format into their PDMS products. Some other companies had added XGL/ZGL exporters into their software such as CATIA, MicroStation and Solid Edge.

As explained on the Okino ZGL import converter page, files can be imported from AVEVA PDMS via the ZGL file format and AVEVA's 'rvm2zgl.exe' program. However, in more recent years, you can export DWF-3D files from AVEVA PDMS and import those files directly into Okino software.

PDB import converter's overview

XGL export converter's overview