The quickest and simplest way to create restriction enzyme generated constructs in MacVector is to use Edit | Copy and Edit | Paste. The strategy to use is identical to copying a paragraph from one Microsoft Word document to insert into a second document. i.e.
Select the restriction enzymes flanking the source fragment in either the Map tab of the sequence window, or the Map Results tab after a Restriction Enzyme analysis. Hold down the [SHIFT] key to select the second enzyme. In circular maps, the selection always proceeds in a clockwise direction, so the order you select is important.
Choose Edit | Copy. This places the fragment onto the system clipboard, along with sticky end information.
Switch to the destination vector. Select the target restriction enzyme site(s). When selecting two sites, make sure you select the fragment you want to replace.
Choose Edit | Paste. If the restriction enzyme site(s) have ends compatible with the copied fragment, this will insert the fragment from the system clipboard into the vector. If the ends are incompatible, you will get a warning “ligation dialog” with options to fill or cut back ends to make them compatible.
The red line around the left ends indicates that they are compatible. If you were to fill or cut back the right hand ends you would see green lines indicating they are now compatible.
MacVector will never let you create an invalid construct, so you can select/copy/paste to create new constructs safe in the knowledge that if the ends are not compatible, MacVector will always show this warning dialog.
One final tip, if a fragment can be inserted in either orientation, hold down the [option] key and the Edit | Paste menu item will change to Edit | Paste Flipped, letting you insert the fragment in the opposite orientation.
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