This command is new in PyMOL 1.6, for older PyMOL versions, check the rigimol scripts.

The “morph” command creates an interpolated trajectory between two or multiple conformations. If the two input objects are not the same, they are matched based on sequence alignment.

Available from the internal GUI: A > generate > morph

morph name, sele1 [, sele2 [, state1 [, state2 [, refinement [, steps [, method [, match ]]]]]]]

name = string: name of object to create

sele1 = string: atom selection of first conformation

sele2 = string: atom selection of second conformation {default: <sele1>}

state1 = int: sele1 state {default: 1}. If state1=0 and sele1 has N states, create N morphings between all consecutive states and back from state N to 1 (so the morph will have N*steps states). If state2=0, create N-1 morphings and stop at last state.

state2 = int: sele2 state {default: 2 if sele1=sele2, else 1}

refinement = int: number of sculpting refinement cycles to clean distorted intermediates {default: 3}

steps = int: number of states for sele2 object {default: 30}

method = string: rigimol or linear {default: rigimol}

fetch 1akeA 4akeA, async=0
align 1akeA, 4akeA
morph mout, 1akeA, 4akeA