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How to convert PDB (Protein Database) to DGN (MicroStation)?

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.

DGN

DGN is a 2D/3D file format, with its roots going back to the early 1980s, that is used as the native file format of such programs as Bentley's MicroStation and Intergraph's PDS software packages. Relative to deep history, DGN could be considered a competitor or rival to the Autodesk DWG file format. Okino considers both DGN and DWG rather "crude" and old file formats, depending on what vintage of file is used and whether the files contain ACIS-SAT/Parasolid "BREP solids" geometry or just 2D/3D vector geometry.

Okino considers a DGN V8 file to be of two varieties: (1) "GIS" like models defined using basic primitives like lines, curves, arcs and 3D objects defined by the extrusion and revolution of these basic elements - these types of files are typically glutted with an enormous number of basic elements which can result in massive scenes that can very slow to display and take up a lot of memory. (2) The second variety of DGN file uses the more modern "BREP solids" geometry type to define the 3D objects as lighter weight and more efficient NURBS surfaces and solids.

Okino spent over 20 years developing its DGN importers and exporters. As such, we understand the nuances of DGN and its related conversion issues. Please refer to our DGN importer WEB page which has extensive information on (1) the history of DGN and when to use DGN, (2) how to import massive DGN files (such as PDMS 3D plants, oil refineries, etc), (3) how to import from AVEVA PDMS and Intergraph PDS, and (4) our suggestions about using STEP or VRML2 as alternative conversion methods from Bentley's MicroStation.

PDB import converter's overview

DGN export converter's overview