The selection interface was added later. After completing the Intro Puzzles, players can switch to the selection interface if desired.
Many tools in the original interface are accessed by hovering the mouse pointer over a segment of the protein and clicking (or right-clicking or shift-clicking) to display a wheel menu. Mutating a single segment in Design Mode is involves a wheel menu, as does assigning secondary structure in Structure Mode, In Pull Mode, many tools that work on specific parts of the protein are available in a wheel menu via right-click or shift-click.
The original interface has a menu bar that runs along the lower left edge of the screen. The menu bar has "Actions" and other sections, which can be expanded to reveal more options.
In general the same tools and options are available in both the original and selection interfaces. The selection interface allows selecting one or more segments for processing, which is much the same as how many recipes work.
One difference involves the wiggle tool. In the original interface, selecting wiggle from the right-click (control-click) wheel menu in Pull Mode, applies the local wiggle tool to the section of secondary structure indicated, and any adjacent loop segments. In the selection interface, the same segments can be selected, but the regular wiggle is applied. Wiggle and local wiggle are different, with "local" wiggle's changes confined to a smaller part of the protein.
Selecting segments in another area of difference. The selection interface allows any group of segments to be selected. The segments do not need to be adjacent. The selection interface also allows segments to be selected in a "sphere" surrounding a starting segment. The user clicks on a starting segment, then shift-clicks and drags the mouse pointer up and down the screen to expand or contract the sphere. The original interface does not have similar capabilities.