Bio-Rad PDQuest 2-D Analysis Software - Manual (Page 49)

5.5 Confirm Cuts
The Confirm cuts button was added to help in checking the cut progress of a fluorescent stained
gel. With visible stained gels, it is easy to look in on the spot cutter to see that the cutting tip is
cutting right on the spot. However, since the spots are not visible without UV illumination in a
fluorescent gel, the "Confirm cuts" operation provides an on-screen method for monitoring the cut
run.
1. After starting the cut run in Basic Excision Tool, let the cut run proceed for 5–10 spot cuts.
2. When you want to check on the cut run, click on "Pause".
3. Click on "YES" to "Confirm Pause run".
4. Click on the "Confirm cuts" button.
5. The camera will acquire a new image and create a floating window on top of the existing
screen.
6. This window will display the gel image with spot "holes" where it has been cut by the spot
cutter. It will also show the overlay circles of the cut targets. The white circles are the
spots that have already been cut, and the green circles are the spots yet to be cut.
Fig. 44. Basic Excision Tool confirm cuts function.
7. You should be able to see "holes" in the spots in the image within the overlay target circles.
Note:
The "snap to peak" and "gaussian fit" targeting features center the cuts on the densest
portion of the spot, not necessarily in the visual center of the spot. If the target circles and cuts
are off center, this does not necessarily mean that the targeting and cuts are off the intended cut.
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