X3D is a boxing program developed by James Conway. It contains a 'help'. If you are lazy, just do the following:
- Run X3D, and open a TIFF image file using the "File"->"Open Image" menu.
- Select a particle using the mouse. Then change the radius to a suitable value (the 'Pick radius' is just a visual help).
- 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.
- 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).
- Save the selected coordinates in a file .crd
- Select the Preprocess->Run menu item, this will extract, preprocess and save all the selected particles to image files.