56 lines
1.6 KiB
Python
56 lines
1.6 KiB
Python
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'''
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Various morphing workflows
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(c) 2013 Schrodinger, Inc.
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(c) 2011 Thomas Holder
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(c) 2009 DeLano Scientific LLC.
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'''
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import pymol
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cmd = __import__("sys").modules["pymol.cmd"]
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def morph(name, sele1, sele2=None, state1=-1, state2=-1, refinement=3,
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steps=30, method='rigimol', match='align', quiet=1, _self=cmd):
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'''
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DESCRIPTION
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Creates an interpolated trajectory between two or multiple conformations.
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If the two input objects are not the same, match them based on sequence
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alignment.
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This command supports two methods: rigimol and linear. RigiMOL is an
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incentive feature and only available to official PyMOL sponsors. Linear
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morphing is quick and robust but likely to produce distorted intermediates.
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ARGUMENTS
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name = string: name of object to create
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sele1 = string: atom selection of first conformation
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sele2 = string: atom selection of second conformation {default: <sele1>}
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state1 = int: sele1 state {default: 1}. If state1=0 and sele1 has N
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states, create N morphings between all consecutive states and back from
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state N to 1 (so the morph will have N*steps states). If state2=0, create
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N-1 morphings and stop at last state.
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state2 = int: sele2 state {default: 2 if sele1=sele2, else 1}
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refinement = int: number of sculpting refinement cycles to clean
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distorted intermediates {default: 3}
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steps = int: number of states for sele2 object {default: 30}
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method = string: rigimol or linear {default: rigimol}
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EXAMPLE
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fetch 1akeA 4akeA, async=0
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align 1akeA, 4akeA
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morph mout, 1akeA, 4akeA
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'''
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raise pymol.IncentiveOnlyException()
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# vi: ts=4:sw=4:smarttab:expandtab
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