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The programs on the web site are archived into a "stuffit" self extracting file; thus the use of the ".exe" file extension on the download package. After the download transfer is complete, you should "double-click" the .exe package and move the programs (mage.exe, prekin.exe and/or probe.exe) to your kinemage work area. The self-extracting archive route was chosen instead of the common zip archive system found on Windows OS because: 1) we were still finding that some users did not have a zip archive utility program and 2) confusion arising with the ability to run programs within zip archives.

This document attempts to explain a setup on the various Windows OS (98, 2000, Me, XPn, etc.) which allows mage, prekin, and probe to communicate so that the "remote update" functionality found in mage works allowing model adjustments using our all-atom contacts methods. The steps we recommend may be overly simplistic and not using Windows OS capabilities well. This is due solely to our ignorance and unfamiliarity with Windows. For this we apologize, and, offer up these learnings about Windows-based setup hard-won from our students who use Windows.


Communication between mage, prekin, and probe on a Windows box must address two conflicting requirements: 1) apparently an executable program requires an ".exe" extension - an imposition placed by the OS and 2) our programs are internally invoked by their simple names, e.g. mage calls "prekin" and not "prekin.exe". Added on top of this is a potential source of confusion: the system option of hiding "common" file extensions. These potential problems can be avoided by these measures:

  • keep all the kinemage-related files - programs, shortcuts, *kin and *.pdb files - in one folder;
  • set the folder view option so that it displays all file extensions;
  • ensure that the programs have an ".exe" extension - and only one (no mage.exe.exe!); and
  • create and keep in this folder a shortcut to each program, and name the shortcuts with the simple program name - a shortcut named "mage" for example.

Suggested Install

  1. You have to specify to save the download to disk, and depending upon internet browser set-up perhaps where to put it. Mage, prekin and probe come in separate download archives; so, if you want all three programs, you'll need three downloads. Either create one folder for all 3 downloads, or 3 folders to hold them separately and then combine after extraction.
  2. After placing the download archive into a folder, double-click the archive to start the self-extraction. You'll be asked where to extract the archive files and whether or not to overwrite this text file, which is in each archive. After extraction, you should have an .exe file (the program) and this .txt file.
  3. Repeat steps 1 & 2 for each program you want (mage, prekin, and probe). When done, combine all three .exe files into one common folder. Insure that this folder's view options display extensions for all files. Insure that the programs have an .exe extension. Create a shortcut to each program within the same folder. Rename the shortcuts with the simple program name: mage, prekin, probe.


  1. With the programs - named as mage.exe, prekin.exe, and probe.exe - and their shortcuts - named as mage, prekin, and probe - residing at the same level in a common folder, all the needed intra-communications should be functional.
  2. Mage can be started by:
    • either double-clicking the mage.exe icon or the mage shortcut icon, or
    • dropping a kinemage file onto either the program icon or shortcut icon.
  3. Likewise, Prekin can be started by:
    • double-clicking the program or shortcut icons or
    • dropping a PDB file onto either Prekin icon.
    Prekin is also invoked by mage for mage's remote update functions.
  4. Probe is invoked by mage's remote update functions.

Kinemage files can be gotten from our website or others, from running Prekin to make your own, from writing one by hand, and from our MobProbity web server. Our website and MolProbity can be reached at http://kinemage.biochem.duke.edu.