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What are PDB Files?
The PDB file extension is used by several different applications, which are not necessarily interchangeable. Because of this, you will need to know where the PDB file originated. For example, if you work in the BioTech industry and a colleague sent you a PDB file related to his research on proteins, then it’s a safe bet that this particular PDB file is a “Protein Data Bank” file. On the other hand, if your accountant sent you a PDB file, the file would more likely be related to Quicken software.
The four primary PDB file types are:
- Protein Data Bank Files - This file extension is used by the Research Collaboratory for Structural Bioinformatics. It contains the 3D coordinates of a protein’s (or another chemical compound’s) atoms.
- Program Database Files - This is a database format used by Quicken, Pegasus, and Microsoft Visual Studio.
- Palm Desktop Database Files - This format is used by Palm-based PDAs and can contain data such as spreadsheets, documents, maps, and images.
- Power Designer Backup Files - These files are backup files of a Sybase PowerDesigner database.
Opening PDB Files
If you don’t know where the file originated, it’s going to be tough to figure out which type of program to use to open your PDB files. Start by trying to open the file with a text editor such as NotePad. If the file opens, you may be able to find clues that lead you to the correct program. The most common type of PDB file is as a program database file. If you have Quicken or Microsoft Visual Studio.net, try opening the file with those applications.
If you suspect that the file is a Palm Desktop Database file, use PRODEC Desktop PDB Viewer or LLUSoft’s PDB Explorer.
PowerDesigner Backup files are to be used to restore a damaged Sybase PowerDesigner database. In order to work with these files, you will need the PowerDesigner software.
If the PDB file is a Protein Data Bank file, use QuickPDB or find an add-on for Microsoft Internet Explorer such as Protein Workshop or Jmol to open it. The University of Massachusetts Web site lists a variety of viewers and plugins.
