Run digests and virtual gels

The enzyme panel lists which enzymes cut your plasmid and digests it with the ones you pick. The virtual gel shows the expected bands next to a ladder.

Digest a plasmid

1. Open the plasmid.
2. Press Ctrl/Cmd+K and run Open Enzyme Panel. It also sits under Search & Analysis in the tools list (click Editor on the left rail).
3. On the Enzymes tab, Cuts this plasmid lists every enzyme that cuts. Filter with Search enzymes... or the cutter menu, such as Single Cutters.
4. Tick one or more enzymes and click Run digest.
5. The Digest tab shows a gel next to a fragment table.

The fragment table lists each fragment's Ends (which enzyme cut each side), Coordinates, Length and Features. Click Coordinates or Length to sort.

Check buffer compatibility

1. Select at least two enzymes.
2. Open the Digest tab to see Overall Compatibility and Pairwise Compatibility.

Add a custom enzyme

1. In the enzyme panel, switch to Full catalogue.
2. Click Custom Enzyme.
3. Fill in Enzyme Name, Recognition Sequence (IUPAC codes allowed), Cut Pos (Fwd) and Overhang Type, then click Save.

Run a virtual gel

1. Open the plasmid, press Ctrl/Cmd+K, and run Open Virtual Gel.
2. Click Add Sample. Pick a plasmid under From Library, or enter a name and size under Manual Entry.
3. On a plasmid lane, click Digest... to cut it with enzymes.
4. Under Parameters, set Agarose, Voltage, Run Time, Buffer and DNA Ladder.
5. Open Results for band sizes and migration.

Show sites on the map

Run Restriction Analysis from the command palette. It turns on the enzyme layer of the map. It does not open a window or run a digest.