Opening a PDB File

The PDB file type is primarily associated with Visual C++.

PDB	File extension: PDB
	File type:	program database file

What is a PDB file?

PDB files mostly belong to Visual C++ by Microsoft. PDB is a textual file format describing three-dimensional structures of molecules held in the Protein Data Bank. It provides descriptions and annotations of protein and nucleic acid structures including atomic coordinates, secondary structure assignments, as well as atomic connectivity. It also stores experimental metadata.

Structure: A typical PDB file describing a protein consists of hundreds to thousands of lines describing the following records:

HEADER, TITLE, and AUTHOR - information about the researchers who defined the structure;
REMARK - free-form annotation; can accommodate standardized information;
SEQRES - sequences of peptide chains;
ATOM - coordinates of the atoms that are part of the protein;
HETATM - coordinates of hetero-atoms.

Related extensions: PDB files can also be saved as ENT or BRK. Legacy: PDB is now considered a legacy format, being replaced by the newer mmCIF (extension: CIF) file format.

Related associations: PDB could also refer to Microsoft's program database file - a proprietary file format for storing debugging information about a program.

How to open a PDB file

You need a suitable software like Visual C++ to open a PDB file. Without proper software you will receive a Windows message "How do you want to open this file?" or "Windows cannot open this file" or a similar Mac/iPhone/Android alert. If you cannot open your PDB file correctly, try to right-click or long-press the file. Then click "Open with" and choose an application. You can also display a PDB file directly in the browser:. Just drag the file onto this browser window and drop it.

Online PDB File Viewer

Choose your .pdb file to view this image

or drag and drop it here

Online File Viewer

✈

Read our privacy guarantee in Filext’s terms and privacy policy

Please allow ads on our site

This helps us keep our servers running. Then re-upload your file to view it.

Click here to see how to disable the ad blocker for filext.com

How to convert PDB files to JPG, PDF, HTML, DOC, ...

You can convert PDB files using our online PDB file viewer (powered by Convert.Guru):

Just click the "Choose your .pdb file to view this image" button on this page.
After your file is opened in browser,
click "Save as..." in the menu.
Then click the file format (e.g. PDF, JPG, DOCX, TXT, ...) you want.
Your file will be converted and downloaded.

Programs that open and convert PDB files:

Visual C++ by Microsoft
See the previous paragraphs to learn more about the main application. PDB files are often referred to as Visual C++ databases because this type of file is primarily created or used by this software.
Avogadro
Avogadro is a free and open source 3D molecule editor and visualizer. The program uses PDB files to store the coordinates of atoms within a protein. These files are also used by the Protein Data Bank, a worldwide repository for the processing and distribution of 3D biological macromolecular structure data. This file format is classified as Data. Related links: Manual, Wikipedia
BGBlitz (positional database file) by Frank Berger
BGBlitz is a professional backgammon software developed by Frank Berger. The program stores positions of game objects within a PDB file. This file format is classified as Database. Related links: FAQ, Installation instrucitons, Backgammon links
Commodore 64 Emulator (Commodore 64 emulator data file) by Commodore
The Commodore 64 was an 8-bit home computer, developed by Commodore International. Emulators can be used to simulate devices such as the Commodore 64 on modern hardware. PDB files were used by a Commodore 64 emulator for storing data, however, they now appear obsolete and no longer used by any emulator. This file format is classified as Data. Related links: Wikipedia, C64 Wiki, Commodore Wikipeida
Insight II by Accelrys
Insight II was a molecular modeling environment developed by Accelrys, which provided a graphical interface to algorithms for molecular dynamics, homology modeling, de novo design, and electrostatics. Related links: Guide, Manual
MolMol (molecule description file) by ETH Zürich
MolMol is an open-source project developed for displaying, analyzing, and manipulating 3D molecular structures. The program uses PDB files to store molecule descriptions. This file format is classified as Simple text file. Related links: Science Direct article, Reference manual
Palm OS (Palm OS database file) by Palm
Palm OS was a mobile operating system developed for mobile devices. The operating system has since been discontinued. Palm OS used PDB files as a container for storing databases. This file format is classified as Database. Related links: iSilo, Wikipedia
Pegasus Multimedia DataBase (program database file) by Euro Sistemi Srl
Pegasus Multimedia Database is a program developed by Euro Sistemi for managing optical archives, electronic documents, and multimedia data. The program uses PDB files to store databases where this information is saved. This file format is classified as Database.
PhotoDeluxe (image file) by Adobe
Adobe PhotoDeluxe was a program used for editing 2D images. The program has since been discontinued and is no longer sold by Adobe. PhotoDeluxe was compatible with images stored using the PDB files, which could be opened and edited using the program. This file format is classified as Raster Image. Related links: Wikipedia, Adobe PhotoDeluxe Revisited
PowerBASIC (debugger symbols file) by PowerBASIC
PowerBASIC is a family of compilers for the BASIC programming language. The compilers use PDB files for storing debugging symbols. This file format is classified as Data. Related links: Which Compiler should I choose?, Wikipedia
PowerBuilder (dynamic link library file) by Sybase
PowerBuilder is a program originally developed by Sybase, which is now owned by SAP and managed by Appeon. The program is used to create high performance data-driven applications. PDB files are dynamic link libraries used by PowerBuilder, similar to a DLL file for most Windows applications. This file format is classified as System. Related links: Wikipedia, Documentation
PowerDesigner (model backup file) by Sybase
PowerDesigner is a program developed by Sybase, which has since been acquired by SAP. The software is used for modeling data and processes for data architecture, information architecture, and enterprise architecture. The program stores backups of models as PDB files. This file format is classified as Backup. Related links: Sybase Wikipedia, PowerDesigner Wikipedia
Powerproject Teamplan by Elecosoft
Powerproject is a program sold by Elecosoft for managing construction projects. The program stores data in a PDB file. This file format is classified as Data. Related links: Tutorial video, YouTube channel
QuickPOS
Ribbons (protein data bank file) by Mike Carson
Ribbons was a program developed by Mike Carson for rendering 3D molecules as images. The program uses coordinates stored as a protein data bank file, using the PDB extension to create images of molecular models. This file format is classified as Data. Related links: User Guide, Manual
TACT
TACT, or Text Analysis Computing Tools, is a tool for researchers which performs text retrieval and analysis on literary works. Related links: TACT description, Manual
TealPaint (image file) by TealPoint
CADSTAR is Zuken's Windows-based desktop PCB Design solution, that is ready-to-use and easily integrated into your current design environment while preserving your legacy data. The PCB files contain the layout that is used for printing the physical board, where it is saved in standard ASCII text format. This file format is classified as Raster Image. Related links: XnView, Manual
XnView (image file) by XnSoft
XnView is a free program developed by XnSoft for viewing and editing images. The program contains many features for modifying images and supports all major image formats. PDB image files can be viewed and edited using XnViewer. This file format is classified as Raster Image. Related links: Wikipedia, User Guide

PDB format details:

If you know the file format, you can also find out how to open or edit the file. Often, the file format can be deduced from the file extension or the initial bytes (called the signature). However, different programs can use the same file extension, and file extensions can be assigned incorrectly. So you need a detailed analysis of a file to find out the format and the associated program. Below you will find our evaluation of the PDB files:

PDB is a very common file type and includes different formats for different programs. However, the following two file formats are common:

45% of all PDB files use the same file format, which have the signature Microsoft C/C++ . The content consists of illegible binary data, which can only be read and interpreted by the associated programs. The average file size is 380 KB with most files being between 34 KB and 8 MB in size. The file type was developed 10 years ago and is still in use today. The following keywords are characteristic: Microsoft C/C++ MSF 7.00. These files can be linked to registered, apple, server, windows, service, trumpf, user, player and base.
9% of all PDB files start with the magic bytes BSJB, which are always the first bytes of this file format. If you open these files in a text editor, you will see only illegible characters. The files are 1 KB to 240 KB in size, with a median of 21 KB. The keywords #Blob, #GUID, #Pdb, #Strings, BSJB and PDB v1.0 are typical for these files. A usual file name is Assembly-CSharp.pdb or Assembly-CSharp-firstpass.pdb. Such PDB files store data about unity, engine, assembly, csharp, module and manager.

All the rest of the PDB files (46%) have different formats, such as XML, HEADER, ATOM, REMARK, ObjStore, COMPND, TITLE and CRYST. Often described as epdf, unrelaxed, textbook, medicine, nutricion or export. You can get all the details of your PDB file by dragging it onto this page or by clicking the button "Choose your .pdb file to view this image" above.

Technical Data for PDB File Extension

File classification:

Database

Related files:

pbd, pdp, dll, exe, palm, pdm, dbp, ilk, idb, dpb, epdf, config, mol2, pnb, zip, ent, bdb, pbt, prc, pgb, dsw, dbg, vcw

Mime type:

chemical/x-pdb, application/vnd.palm, application/octet-stream

The following listing is compiled from the database produced by the 'Associate This!' program, selected data from the main FILExt database and file extension information submitted by users.

ProgramID: GraphicsConverterPro.pdb, FileType: TealPaint, AppName: GraphicsConverter-reg
EXEFile: GraphicsConverter.exe

ProgramID: ICPlus, AppName: ImageEditor Plus
EXEFile: ICPlus.exe

ProgramID: PalmQuickInstall.PdbFile, FileType: Palm Database File, AppName: Palm Quick Install Module
EXEFile: QuickInstall.exe

ProgramID: pdbfile, FileType: Intermediate file

ProgramID: pdbFile, FileType: Palm Database File, AppName: Install Tool Application
EXEFile: Instapp.exe

ProgramID: pdbfile, FileType: Program Debug Database

ProgramID: PrintShop.Project, FileType: Print Shop Project, AppName: Home Productivity Program

ProgramID: Demo Builder
EXEFile: %ProgramFiles%\Demo Builder\db.exe %1

ProgramID: pdbFile
EXEFile: %ProgramFiles%\Clie\Instapp.exe %1

ProgramID: pdbFile
EXEFile: %ProgramFiles%\Handspring\Instapp.exe %1

ProgramID: pdbFile
EXEFile: %ProgramFiles%\Palm\Instapp.exe %1

ProgramID: pdbFile
EXEFile: %ProgramFiles%\Sony Handheld\Instapp.exe %1

ProgramID: pdbFile
EXEFile: C:\Palm\Instapp.exe %1

ProgramID: pdbfile
EXEFile: f:\utils\handspring\Instapp.exe %1

ProgramID: pdbFile
EXEFile: C:\Palm\Instapp.exe %1

ProgramID: pdbFile
EXEFile: %ProgramFiles%\Sony Handheld\Instapp.exe %1

ProgramID: pdbfile
EXEFile: %ProgramFiles%\Informax\Vector NTI Suite 9\3D-Mol.exe %1

ProgramID: pdbFile
EXEFile: %ProgramFiles%\palm\Instapp.exe %1

ProgramID: pdbFile
EXEFile: %ProgramFiles%\Internet Explorer\Iexplore.exe %1

ProgramID: XnView.Image
EXEFile: %ProgramFiles%\XnView\xnview.exe %1

ProgramID: PrintShopDeluxe
EXEFile: C:\PSDWIN\psdwin.exe %1

ProgramID: PrintShop.Project
EXEFile: C:\The Print Shop Products\The Print Shop Premier Edition 5.0\Pspe5.exe %1

ProgramID: pdbFile
EXEFile: %ProgramFiles%\Instapp.exe %1

ProgramID: PalmQuickInstall.PdbFile
EXEFile: %ProgramFiles%\Palm\QuickInstall.exe /FileExt

ProgramID: SDDocuments.Atomistic3dDocument.1
EXEFile: %ProgramFiles%\Accelrys\MS Modeling 3.2\Studio\MatStudio.exe

ProgramID: PrintShop.Project
EXEFile: %ProgramFiles%\The Print Shop Deluxe III\psdwin.exe %1

ProgramID: pdbFile
EXEFile: %ProgramFiles%\DeLano Scientific\PyMOL\pymolwin.exe %1 %*

ProgramID: pdbFile
EXEFile: %ProgramFiles%\Palm\Instapp.exe pdf_auto_file

ProgramID: pdbFile
EXEFile: C:\Palm\Instapp.exe pdtfile

ProgramID: pdbfile
EXEFile: %ProgramFiles%\Palm\Instapp.exe PDXFileType

ProgramID: pdbFile
EXEFile: %ProgramFiles%\Sony Handheld\Instapp.exe PDFXMLDesigner.Document

ProgramID: pdbFile
EXEFile: %ProgramFiles%\Sony Handheld\Instapp.exe pdcfile

ProgramID: pdbFile
EXEFile: C:\Palm\Instapp.exe PerfFile

ProgramID: pdbFile
EXEFile: %ProgramFiles%\Palm\Instapp.exe PDFXMLDesigner.Document

ProgramID: PalmQuickInstall.PdbFile
EXEFile: %ProgramFiles%\palmOne\QuickInstall.exe /FileExt

ProgramID: pdbFile
EXEFile: %ProgramFiles%\Handspring\Instapp.exe PerfFile

ProgramID: pdbFile
EXEFile: %ProgramFiles%\Handspring\Instapp.exe PDXFileType

ProgramID: pdbFile
EXEFile: %ProgramFiles%\Palm\Handspring\Instapp.exe PDVDmpgfile

ProgramID: pdbFile
EXEFile: %ProgramFiles%\Palm\Instapp.exe PerfFile

ProgramID: pdbfile
EXEFile: %ProgramFiles%\Invitrogen\Vector NTI Advance 10\3D-Mol.exe

ProgramID: MyViewPad.pdb
EXEFile: %ProgramFiles%\My ViewPad\MyViewPad.exe

Show all 41 listings To Top

a pdb program database file is a special file format by Microsoft and should only be edited and saved with the appropriate software.

How to solve problems with PDB files

Associate the PDB file extension with the correct application.
Update your software that should actually open program database files. Because only the current version supports the latest PDB file format. Search, therefore, e.g. on the Microsoft manufacturer website after an available Visual C++ update.
To make sure that your PDB file is not corrupted or virus-infected, get the file again and scan it with Google's virustotal.com.
Click here to open your .PDB file online - secure, fast, and no downloads needed.