Editing Rigimol.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 to the second conformation.

''Notice: There is a new [[morph]] command in PyMOL 1.6''

== Usage ==

 morph source, target [, first [, last [, refinement [, async [, steps ]]]]]

== Arguments ==

* source = string: name of two-state input object
* target = string: name of output object to create
* first = int: start state of source {default: 1}
* last = int: end state of source {default: 2}
* refinement = int: number of sculpting refinement cycles to clean distorted intermediates {default: 10}
* steps = int: number of states for target object {default: 30}

''Warning: arguments first, last and steps new in PyMOL 1.5 (up to 1.4 they are always at default values)''

== Example ==

<syntaxhighlight lang="python">
# get open and closed conformation of adenylate kinase
fetch 1ake 4ake, async=0

# make two state object
align 1ake and chain A, 4ake and chain A, cycles=0, object=aln
create rin, 1ake and aln, 1, 1
create rin, 4ake and aln, 1, 2

# morph
from epymol import rigimol
rigimol.morph("rin", "rout")
</syntaxhighlight>

== Troubleshooting ==

Rigimol likes to fail if the atom identifiers (like chain) in the two input states do not match properly. A more robust way to create the two state object is to [[update]] state two coordinates without matching identifiers:

<syntaxhighlight lang="python">
# make two state object
align 1ake and chain A, 4ake and chain A, cycles=0, object=aln
create rin, 1ake and aln, 1, 1
create rin, rin, 1, 2
update rin, 4ake and aln, 2, 1, matchmaker=0
</syntaxhighlight>

== PyMOL Command ==

if you prefer PyMOL syntax over python syntax, add this to your [[pymolrc]] file:

<syntaxhighlight lang="python">
import epymol.rigimol
cmd.extend('morph', epymol.rigimol.morph)
</syntaxhighlight>

== See Also ==

* [[morph]], the PyMOL 1.6+ morph command
* [[morpheasy]], a robust wrapper for the morph command which takes care of matching atom identifiers (requires the '''psico''' module)
* [[slerpy]]
* [[eMovie]]

[[Category:Commands]]
[[Category:Modeling_and_Editing_Structures]]