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X3D is a boxing program developed by James Conway. It contains a 'help'. If you are lazy, just do the following:

  1. Run X3D, and open a TIFF image file using the "File"->"Open Image" menu.
  2. Select a particle using the mouse. Then change the radius to a suitable value (the 'Pick radius' is just a visual help).
  3. When finished selecting particles, go to the "Preprocess"->"Parameters" menu and set all the parameters there. Important: Set "File Type" to EZD and use a reasonable box size.
  4. Go to the "Preprocess"->"Set Centering Parameters" menu and set the pixel size (in Angstroms); and set the remaining fields to 1 (we are not going to use them).
  5. Save the selected coordinates in a file .crd
  6. Select the Preprocess->Run menu item, this will extract, preprocess and save all the selected particles to image files.