Does VMD have any molecular editing features?
You can use VMD to move atoms, residues and fragments around via the “Mouse” menu. The text user interface will let you manipulate the atom coordinates in almost any fashion. See the user guide for more information on how to write scripts. It can also be used to change the beta and occupancy information. If you want to build/edit structures beyond what is described above, you’ll need to use the psfgen plugin for this purpose.
