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DNA binding protein

Image of protein bound to DNA JPEG version (85KB), TIFF version (1,547KB)

Overview

This image shows a section of protein bound to DNA.

In order to get both full sized atoms and stick representations into the same image, an intermediate file had to be created.

  1. The orientation desired was chosen in MidasPlus.
  2. Only the DNA was displayed, the orange spheres. These coordinates were put into a file using the "pdbrun"command. command: pdbrun cat > image.file
  3. Then, only display the portion of the coordinates that are desired to be represented as sticks (the yellow and magenta sticks). Use the "preneon" command to put coordinates for creating sticks into a file. These "sticks" are actually hundreds of spheres which the MidasPlus delegate Neon determines in order to create a cylinder between each atomic coordinate. command: preneon cat >> image.file DON'T FORGET TWO ">" SYMBOLS. This is so that the "stick" coordinates will be appended to the image.file you already created, and not completely overwrite the file.
  4. Finally, the MidasPlus delegate program Conic can be used to display the final image. This program must now be run directly on the file, not through MidasPlus.

    Get out of Midas plus. Then from any one of your windows, give the command: conic image.file If you want the file to be saved into an image file, give a command such as: conic -o final.rgb image.file See the Conic manual page for more details on saving output files, etc.

Credits

Image by Julie Newdoll and Tom Kornberg. Published in the Journal of Biological Chemistry, Issue of Dec 25, pages 26813-26816, 1993, Vol 268, #36, "Understanding the Homeodomain", Thomas B. Kornberg. ©2004 The Regents, University of California; all rights reserved.