When performing an agarose gel simulation, the Settings panel, represented by a gear icon ( ), is located on the lower right of the Document window. This panel lets you change properties of the simulated agarose gel displayed in the Gel Simulation view.
The Settings panel is only available after using the File > New Agarose Gel command, and can then be accessed by clicking on the Settings tab.
- Brand – Use this drop-down menu to choose the gel manufacturer.
- Type – Use this drop-down menu to select the “model” of gel from the Brand manufacturer. The choice made here affects the lane layout, which includes the next three settings below.
- Lanes – By default, the number of lanes is determined by the selections made in Brand and Type. However, you can type in a different value, if desired.
- Combs – When using agarose gels, combs are plastic inserts with teeth, each the width of one lane. The spaces between the teeth are equal to the spaces between the lanes. By default, the number of combs in the Settings panel is determined by the selections made in Brand and Type. If desired, you may type in a different value. Numbers greater than 1 cause duplicate sets of lanes to appear in the Gel Simulation view.
- Area – By default, the area of the gel is determined by the selections made in Brand and Type. However, you can type in any desired Width and Length, in cm.
- % Agarose – The concentration of agarose controls the distance that fragments propagate in a given time. A higher concentration causes fragments to slow down. Therefore, to resolve larger DNA fragments, use a lower % Agarose, and vice versa. By default, % Agarose is set to “1.00.” If desired, make another selection from the drop-down menu.
- Run Time – Use the slider to select a run time between 1-180 minutes. Or type in a number to define a run time of any length.
- Blur – Check this box to slightly blur the bars in the Gel Simulation view, more closely approximating the look of a lab-produced gel. This option is checked by default.
- Smile – Check this box to make the bars in the Gel Simulation view take on a slight “smile” shape, more closely approximating the look of a lab-produced gel. This option is checked by default.
- Reticle at mouse – Check this box to add a blue line that travels vertically with the mouse as it hovers over lanes in the Gel Simulation view. This option is unchecked by default.
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