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How to convert PDB (Protein Database) to DWG (AutoCAD, DXF)?

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.

DWG

DXF and DWG are the native file formats of the Autodesk AutoCAD product since 1982. DWG is the binary file variation to the ASCII DXF file format. These files can be viewed by many programs including Autodesk's free DWG TrueView application. It is a closed file format but has been documented by the Open Design Alliance.

At Okino we consider DXF/DWG to be one of the worst 3D file formats when translating 3D model data between applications (depending on its contents). There is very little understanding about this in the 3D graphics world. As outlined in our "CAD Data Sourcing Suggestons and Rules" page you should ideally use the DWF-3D file format when sourcing from either AutoCAD, Navisworks, Revit and optionally Autodesk Inventor.

Due to deep history, Autodesk software can embed ACIS SAT "BREP solids" data in some of its DXF/DWG files. This is the ideal case as the "BREP solids" geometry definitions lead to cleaner and higher fidelity MCAD file conversions. But even so, it would generally be a safer bet to use a STEP AP214 or "IGES BREP solids" file in such cases.

PDB import converter's overview

DWG export converter's overview