Acquire points

1. Open the acquired square image by double clicking in the navigator window onto the line of your square ( XXX-A; Blue point; named Map1; comment squares.mrc)

2. In navigator window click Add point. Select all holes you want to image by left click in the map. When finished click Stop Adding in navigator window. (Hint: The backspace removes your last selected hole)

Repeat step 1 and 2 for all square maps

3. Afterwards you can delete specific points in the navigator window by highlighting them and clicking “Delete Item”. Hint: Use the checkbox “Collapse group” to either see all hole points of a square in one group or separate items.

4. Click on the tab File –> Open New

5. In file properties set “maximum number of sections” high. I.e. 9999. This is the limit of images that will be taken in the session. Confirm with “OK”.

6. Create the file name averages.mrc in your working directory. Confirm with “Save”.