Mac/PCMolecule: PDB File Information

Many Protein Data Bank (PDB) files contain very large molecules. Some of these molecule files contain over 10,000 atoms! MacMolecule and PCMolecule can read and display the molecules defined in PDB files extremely quickly (for many files two times faster than any other programs available). At the bottom of this page is system information for users of MacMolecule and PCMolecule regarding PDB files and configuration of your browser to automatically view them. Below are a few of the most popular sources of PDB files on the web.

Sources of PDB Files on the Web

Protein Data Bank

What better place for Protein Data Bank files than the official home of the PDB file format? The Brookhaven Protein Data Bank has two excellent pages for searching their extensive inventory of molecule files. They are the detailed WWW Browser or the ever growing and easy to use 3DB Browser. The PDB Help Desk is also a superb and friendly source of advice if you are having trouble locating your favorite molecule.

"Chemistry 1" Structures

An assortment of molecule types, including, but not limited to illustration of Lewis electron dot method, illustration VSEPR, illustration of hybridization, conformers, and isomers, illustration of transition-metal complexes, and illustration of binary ionic substances. This page also contains links to other databases of PDB files.

Klotho Biochemical Compounds Declarative Database

A database of 439 unique biological compounds. The "contents" of individual molecule files can be downloaded in PDB file format.

NTP Chemical Structures

Structures from Published Technical Reports at the National Toxicology Program of the National Institutes of Health. More than 450 structures available in PDB and gif format. Either search by name, or go directly to lists sorted either by TR number or alphabetically.

Molecules from Chemistry at Okanagan University College

Excellent source of small molecule models created by Dr. Dave Woodcock.

Smells Database

University of California, Berkeley database for compounds with interesting smells.

Library of 3D Molecular Structures

New York University Scientific Visualization Center

Macintosh Information

Any file that does not have a MacMolecule file type is recognized as a PDB file. So if a Macintosh file does not have a molecule document icon, it will be recognized as a PDB file. If you would like to directly double click PDB files from the Finder, drop the PDB file onto the utility "Drop for PDB File Type". This can be downloaded from our utilities download page. Likewise, the utility named "Drop for MacMolecule File Type" will force MacMolecule to assume the file is in its own native format, and not a PDB file.

Windows Information

The Windows operating system uses a four character extension at the end of a file to determine file type. The extension for PDB files is ".pdb". The extension for Mac or PCMolecule files is ".mcm".

Configuring Your Web Browser

Your Macintosh or Windows based web browser can be configured to open Mac/PCMolecule files, or PDB files, directly off of a web page. The easiest way to do this is to download a file of the proper type from our forum or from one of the links below. When the file is downloaded, your browser will ask you which program you would like to view the molecule in. Just select MacMolecule or PCMolecule.

If your browser does not ask you which program to open your file in, your browser may have been previously configured to use a different program instead. In this case, you must update the MIME type in your browser's preferences. Below is the official MacMolecule/PDB MIME type information.

   Mac/PCMolecule MIME Type:    chemical/x-macmolecule

   Mac/PCMolecule extension:    .mcm

   (Macintosh Only, File Type:  TEXT)

   

   Protein Data Bank MIME Type: chemical/x-pdb

   Protein Data Bank extension: .pdb

   (Macintosh Only, File Type:  PDBt)