Morph - Revision history

Cchem: 1 revision

2018-12-10T03:24:49Z

1 revision

2018-11-27T10:25:18Z

sculpting terms

2016-06-27T02:04:46Z

1 revision

2016-06-07T16:08:23Z

Refinement

2016-02-08T05:26:40Z

1 revision

2016-01-30T06:03:05Z

2015-08-14T17:32:07Z

1 revision

2015-07-19T03:31:20Z

"match" argument

2014-04-09T20:53:56Z

3 revisions

2014-04-09T17:33:11Z

@@ Line 77: / Line 77: @@
 import epymol.rigimol
 epymol.rigimol.refine(5, "mout")
 </syntaxhighlight>

@@ Line 57: / Line 57: @@
 align conf1, conf2
 morph mout, conf1, conf2, match=in, refinement=0
 </syntaxhighlight>
@@ Line 66: / Line 86: @@
 * [[rigimol.morph]]
 [[Category:Commands]]
 [[Category:Modeling_and_Editing_Structures]]

@@ Line 36: / Line 36: @@
 === 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.
+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 all molecules that are not connected to the protein backbone bounce around; that's why '''refinement=0''' might give better results in this case.
 <syntaxhighlight lang="python">

@@ Line 17: / Line 17: @@
 * steps = int: number of states for sele2 object {default: 30}
 * method = string: rigimol or linear {default: rigimol}
 == Example ==
 <syntaxhighlight lang="python">
@@ Line 24: / Line 32: @@
 align 1akeA, 4akeA
 morph mout, 1akeA, 4akeA
 </syntaxhighlight>

← Older revision		Revision as of 17:33, 9 April 2014
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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 to the second conformation.	+	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.''		''This command is new in PyMOL 1.6, for older versions see [[rigimol.morph]], which requires some scripting.''

← Older revision	Revision as of 03:24, 10 December 2018
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← Older revision	Revision as of 02:04, 27 June 2016
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← Older revision	Revision as of 05:26, 8 February 2016
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← Older revision	Revision as of 17:32, 14 August 2015
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← Older revision	Revision as of 20:53, 9 April 2014
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