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The morph command is an incentive PyMOL feature (not available in open-source version). Given two or more conformations, either as two objects or one multi-state object, morph can create an interpolated trajectory from the first to the second conformation.

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



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



Default Parameters

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

Morphing with Ligand

Since the default match=align method ignores ligands in most situations, we'll use the "in" match method. In this case, both input structures need matching identifiers. The default post-RigiMOL sculpting refinement tends to let bounce around all molecules which are not connected to the protein backbone, that's why refinement=0 might give better results in this case.

# get two hemoglobin beta chains, the "ligand" will be the heme hetero group
fetch 1hbb, async=0
create conf1, chain B
create conf2, chain D
delete 1hbb
# important: identifiers must be the same
alter conf2, chain="B"
alter all, segi=""
# optional: styling
as cartoon
show sticks, not polymer
show nb_spheres
# superpose and morph
align conf1, conf2
morph mout, conf1, conf2, match=in, refinement=0


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

See Also

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