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How to convert PDB (Protein Database) to SpaceClaim (.scdoc)?

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.

SpaceClaim

SpaceClaim is a multipurpose 3-D solids modeling application providing efficient solutions to common modeling tasks. Built on the direct modeling technology, SpaceClaim removes geometry problems associated with various 3-D CAD operations, such as design or concept modeling, repair of translated CAD files, general model defeaturing, and complete model editing.

SpaceClaim provides for a good selection of 3D import and export file formats (which can be found on their "SpaceClaim supported formats" PDF file). Exporting from SpaceClaim into Okino software can be done with any number of 3D file formats such as: ACIS SAT, IGES (186-entities is best), JT, Parasolid x_t, Rhino 3dm, SketchUp, STEP, VRML or Wavefront OBJ. Out of this list a safe bet would be to use STEP AP214, IGES BREP solids (186-entities) or JT CAD files. For non-CAD files, either VRML2 or Wavefront OBJ.

Exporting from Okino software into SpaceClaim can be done with JT, Rhino 3dm, VRML or Wavefront OBJ.

PDB import converter's overview

Vist the SpaceClaim WEB site

JT export converter's overview