Getting Unremediated PDB Files
Repaired March 30, 2009 (to correct a URL that was changed by the Protein Data Bank).
The main reason for getting unremediated PDB files is that when the remediated PDB files contain DNA, Protein Explorer (and perhaps some other software) does not display the DNA properly. If the PDB file does not contain DNA (protein, RNA, solvent and ligands are OK), you probably don't need the unremediated file.
- Download the unremediated PDB file by entering the
PDB identification code here:
and saving the file pdbxxxx.ent.Z (where xxxx is your PDB code) to your disk.
- Note that 1d66 and 1lcd, as displayed from PE's front door with Quick-Start links, are already unremediated.
If your PDB file was published after August 1, 2007, it will not be available in unremediated form!
Double click the downloaded file to decompress it. This should be handled with
WinZip (or with Stuffit Expander on Macs).
Rename the file from pdbxxxx.ent to xxxx.pdb. For example, if you downloaded pdb1d66.ent, rename it to 1d66.pdb.
At Protein Explorer's FrontDoor, start Empty Explorer, then use the Browse button on the Load Molecules control panel
to display your unremediated PDB file.
- Firefox: you'll need to use a downloaded copy of PE.
Alternatively, you can put the unremediated PDB file on a server, and provide a link to display it in the online PE in Firefox. For example, if you put the file at http://home.comcast.net/~joe.blow/109d.pdb, the link would be
http://proteinexplorer.org/pe.htm?id=http%3A//home.comcast.net/~joe.blow/109d.pdb (this is a fictious example and will not work).
Internet Explorer 6: you can use the online PE.
Proceed to the Protein Explorer FrontDoor