Due to morphinator has no time dimension you can put the number of steps proportional to each other to illustrate the rates for each step. Unfortunately the coordinate transformation is linear. By addind the Acceleration value we can speed the transformation up or down over the morph. If < 1 then the transformation starts at a fast pace and slows down and if 1 < it starts slow but speeds up. If i only want this to happend for an arbitary amount of steps (say we have 20 steps all together) then write 1-10,0.9,11-20,1.... (1-10 are the steps), 0.9 is the acceleration factor and 11-20 is the remaining steps and 1, is the default value indicating no acceleration happends what so ever.

This mostly allways has to be done in either Morphinator or in an external program. Often the proteins are in two unique coordinate systems so they must be aligned. You can superpose to a PDB file in the morph seqeunce or something else from the protein databank or upload your own PDB file. To the right you can add what interval of residues too superpose too plus the chain id . (e.g: 1 100 A ).

Forcefields can relax crystral structures so it reduces its energy. This can be ticked to relax the crystal structure before processing.

Morphinator is a semi emperical method to illustrate the trajectory of a protein going from state A to B. The core concept is a linear Morph with a geometrical optimization.
The original Morphinator was designed by Jesper Lykkegaard Karlsen. Morphinator v2 was rewritten in Python and a online interface was added with additional features. The v2 Morphinator was designed by
Jonathan Juhl, Jesper Lykkegaard Karlsen and Thomas Boesen.