Kinetic images, or kinemages, are images of molecules derived from the atomic coordinates of the 3-dimensional structures, that can be moved on the computer screen. This movement gives an impression of a 3-dimensional object. Drs. David and Jane Richardson at Duke University have written and developed the programs MAGE (for viewing kinemage files) and PREKIN (for generating a kinemage file from the atomic coordinates of a 3-dimensional structure of a molecule). These programs are freely available and can be obtained from the Richardson's website:
Click here to go the website for MAGE and PREKIN
At our BMB400 web site, we provide links to the programs and to some kinemage files that we have collected or generated for use in class.
Kinemage files are simple text files that you can import to your computer and view with MAGE. When you click on the links below, you will get a moderately large text file. To make this into something that the MAGE program can read and show, you need to do the following.
1. Click on the file for the molecule you are interested in, e.g. "B-form
DNA kinemage"
2. Select all the text in the file.
2. Copy it onto a clipboard.
3. Open a new file in a text editor on your computer (e.g. Microsoft
Word).
4. Paste in the text from "B-form DNA kinemage".
5. Save it as a "text only" file on your computer, and use .kin as
the suffix for the filename, e.g. "B-DNA.kin"
6. Launch the program MAGE.
7. From MAGE, open the kinemage file on your computer (e.g. "B-DNA.kin")
and you should have an image and information about the molecule.
Demonstration of kinemages
Demonstration
file
DNA and RNA
B-form
DNA kinemage
A-form
RNA/DNA kinemage
Z
DNA kinemage
DNA polymerases
E.
coli DNA polymerase I, Klenow fragment, kinemage
E.
coli DNA polymerase III, beta subunit, kinemage
Mammalian
PCNA kinemage
RNA polymerases
T7
RNA polymerase kinemage
E.
coli RNA polymerase, alpha subunit, kinemage
Ribozymes
Group
I ribozyme kinemage
Transcription factors
Lambda
repressor kinemage
lac
repressor kinemage
TBP
complexed to DNA, kinemage
3
C2H2 Zn fingers kinemage
GATA1
Zn finger kinemage
Leucine
zipper in GCN4, kinemage