When you create a bond between two elements on the canvas and this bond cannot be formed unambiguously, the "Create/Edit bond" dialog will appear.
BioEddie supports both exact bonds and various levels of position variation bonds, e.g. a chemical modification at unknown location of a sequence, or bonds to a specific monomer type of a sequence.
For more information on bond creation see the Create a bond section.
By double-clicking on any monomer its structure will be opened with Marvin JS, Chemaxon's web based chemical sketcher for direct editing. If the modified represents another already existing monomer of the monomer library, it will be replaced by the corresponding monomer , the monomer will be replaced, otherwise a new temporary monomer with a generic identifier will be created locally and on the fly. Such temporary monomers are not persisted when reloading BioEddie in a new session.
For more information on ad-hoc modifications see Create a bond section.
Double-clicking on a component box opens the Sequence Editor dialog where domains can be defined in a specified sequence range by entering the position of the first and the last sequence residue.
For more information see the Editing domains section.