Morph

The morph command is an incentive PyMOL feature (not available in open-source version). Given a two-state object, morph can create an interpolated trajectory from the first two the second conformation.

This command is new in PyMOL 1.6, for older versions see rigimol.morph, which requires some scripting.

Usage

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

Arguments

• 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}

Example

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

GUI

The morph feature is available from the object menu panel: A > generate > morph

See Also

• rigimol.morph