The default settings for the agarose gel display in MacVector generate a reasonable photorealistic simulation of an agarose gel. We have actually boosted the intensity of small bands quite significantly, and reduced their diffusion so that smaller bands show up a little more obviously and crisply than they might in real life. Even so, you may want to adjust the realism if you are trying to visualize small fragments. The simplest way to do this is to click on the Display toolbar button and select “Schematic” from the drop down menu. This will show all of the bands as simple lines at the same intensity. With this, you can be sure that every band is displayed, but many bands that are visible in the MacVector gel may not be visible in your actual gel.
To have finer control over the gel appearance, click on the Prefs button. There is a section of the Preferences dialog (“Gel Simulation Realism”) that is devoted to controlling the realism of the simulation. Try changing those and clicking on the Apply button until you get a simulation you are happy with.
