Jmol/Storymorph: Difference between revisions

The superimpose function works the same way as the Jmol compare function, but it first verifies the required atom selections to prevent Jmol from crashing or freezing. The superimpose function takes two or three parameters. The first paramenter always defines the two structures (see above). The second parameter is either a single domain selection (when calling with two parameters), or it is the list of list describing all domains, with the third parameter an integer designating which domain is to be used in the superposition. The superposition leaves the  first structure in its original orientation and moves the second structure to minimize the distances between corresponding atoms (defined by the domain selection). Different from the morph function, the superposition function alters coordinates for the remainder of the session. Because morphs connect initial and final atomic positions with a path, the orientation of the final state with respect to the initial one is crucial, and the choice of superposition defines this orientation. Said in a different way, you get a different morph if you choose to superimpose the two structures in a different way before starting the morph.