Rigimol.morph - Revision history

Bell: 1 revision

2014-04-09T20:53:56Z

1 revision

Speleo3: fix typo

2014-04-09T17:33:52Z

fix typo

Bell: 4 revisions

2014-03-28T03:49:17Z

4 revisions

Speleo3: see also morph

2013-07-09T15:56:01Z

Speleo3: moved Morph to Rigimol.morph

2013-07-09T15:39:03Z

moved Morph to Rigimol.morph

Speleo3: morpheasy link

2012-07-31T09:11:12Z

morpheasy link

Speleo3: created

2012-05-03T07:56:30Z

created

New page

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.

== 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 ==

* [[psico|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]]

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

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 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.
 == Usage ==
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 == See Also ==
 * [[morpheasy]], a robust wrapper for the morph command which takes care of matching atom identifiers (requires the '''psico''' module)
 * [[slerpy]]

← Older revision	Revision as of 15:39, 9 July 2013
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