Molecular modeling and visualization software - Revision history

Eric Martz: /* Free molecular visualization software */

Eric Martz — Mon, 11 Sep 2023 20:59:34 GMT

Free molecular visualization software

←Older revision		Revision as of 20:59, 11 September 2023
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	*[[Jmol]], an open-source java-based program available in stand-alone or applet forms. The applet is used in Proteopedia, and in the free educational software [[Molecular Workbench]]. Effective use of Jmol requires learning a command scripting language.		*[[Jmol]], an open-source java-based program available in stand-alone or applet forms. The applet is used in Proteopedia, and in the free educational software [[Molecular Workbench]]. Effective use of Jmol requires learning a command scripting language.
-	*[[FirstGlance in Jmol]], an open-source user-interface to [[Jmol]] utilized in the ''3D View'' links in papers in the journal [http://www.nature.com/nature Nature] that report new macromolecular structures. Proteopedia's automatically seeded pages (pages titled with a [[PDB code]]) have links for further exploration of the structure in'' FirstGlance in Jmol''. Although ''FirstGlance in Jmol'' by no means exploits all the power in Jmol, it does show the main structural features of a macromolecule '''without learning any command scripting language'''. [[FirstGlance in Jmol\|More ...]]	+	*[[FirstGlance in Jmol]], an open-source user-interface to [[Jmol]] utilized for a decade in the ''3D View'' links in papers in the journal [http://www.nature.com/nature Nature] that report new macromolecular structures. Proteopedia's automatically seeded pages (pages titled with a [[PDB code]]) have links for further exploration of the structure in'' FirstGlance in Jmol''. Although ''FirstGlance in Jmol'' by no means exploits all the power in Jmol, it does show the main structural features of a macromolecule '''without learning any command scripting language'''. [[FirstGlance in Jmol\|More ...]]
	*[[Chimera]] (free for non-commercial use only).		*[[Chimera]] (free for non-commercial use only).
	[https://molstar.org/ Mol] (MolStar) is offered as a visualization option by the [[wwPDB]]. Its rendering is fast and smooth because it uses [https://developer.mozilla.org/en-US/docs/Web/API/WebGL_API WebGL], and it can handle very large numbers of atoms.		[https://molstar.org/ Mol] (MolStar) is offered as a visualization option by the [[wwPDB]]. Its rendering is fast and smooth because it uses [https://developer.mozilla.org/en-US/docs/Web/API/WebGL_API WebGL], and it can handle very large numbers of atoms.

Eric Martz at 20:58, 11 September 2023

Eric Martz — Mon, 11 Sep 2023 20:58:38 GMT

←Older revision		Revision as of 20:58, 11 September 2023
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	[https://molstar.org/ Mol] (MolStar) is offered as a visualization option by the [[wwPDB]]. Its rendering is fast and smooth because it uses [https://developer.mozilla.org/en-US/docs/Web/API/WebGL_API WebGL], and it can handle very large numbers of atoms.		[https://molstar.org/ Mol] (MolStar) is offered as a visualization option by the [[wwPDB]]. Its rendering is fast and smooth because it uses [https://developer.mozilla.org/en-US/docs/Web/API/WebGL_API WebGL], and it can handle very large numbers of atoms.
	*[https://nglviewer.org/ NGL Viewer] is offered as a visualization option by the [[wwPDB]]. Its rendering is fast and smooth because it uses [https://developer.mozilla.org/en-US/docs/Web/API/WebGL_API WebGL].		*[https://nglviewer.org/ NGL Viewer] is offered as a visualization option by the [[wwPDB]]. Its rendering is fast and smooth because it uses [https://developer.mozilla.org/en-US/docs/Web/API/WebGL_API WebGL].
-	*[https://www.samson-connect.net/ Samson], a powerful visualization and modeling package that is menu-driven. Free for basic use. See demos at [[Sculpting protein conformations]].	+	*[https://www.samson-connect.net/ Samson], a powerful visualization and modeling package that is menu-driven. Free for basic use. See demos at [[Sculpting protein conformations]] and the step-by-step demo at [http://tinyurl.com/sculpting-proteins tinyurl.com/sculpting-proteins].
	*[[Kinemages, Mage and KiNG]] (KiNG = Kinemage, Next Generation) are designed to present the author's viewpoint of a molecular structure. They excel in specialized areas, but are not optimal for general purpose visualization. KiNG can be used in Proteopedia; an example may be seen at [[Hemoglobin#Hemoglobin_subunit_binding_O2]].		*[[Kinemages, Mage and KiNG]] (KiNG = Kinemage, Next Generation) are designed to present the author's viewpoint of a molecular structure. They excel in specialized areas, but are not optimal for general purpose visualization. KiNG can be used in Proteopedia; an example may be seen at [[Hemoglobin#Hemoglobin_subunit_binding_O2]].
	*[[RasMol]], an open-source stand-alone program released in 1993, and still popular. Effective use of RasMol requires learning a command scripting language.		*[[RasMol]], an open-source stand-alone program released in 1993, and still popular. Effective use of RasMol requires learning a command scripting language.

Eric Martz at 20:57, 11 September 2023

Eric Martz — Mon, 11 Sep 2023 20:57:07 GMT

←Older revision		Revision as of 20:57, 11 September 2023
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	[https://molstar.org/ Mol] (MolStar) is offered as a visualization option by the [[wwPDB]]. Its rendering is fast and smooth because it uses [https://developer.mozilla.org/en-US/docs/Web/API/WebGL_API WebGL], and it can handle very large numbers of atoms.		[https://molstar.org/ Mol] (MolStar) is offered as a visualization option by the [[wwPDB]]. Its rendering is fast and smooth because it uses [https://developer.mozilla.org/en-US/docs/Web/API/WebGL_API WebGL], and it can handle very large numbers of atoms.
	*[https://nglviewer.org/ NGL Viewer] is offered as a visualization option by the [[wwPDB]]. Its rendering is fast and smooth because it uses [https://developer.mozilla.org/en-US/docs/Web/API/WebGL_API WebGL].		*[https://nglviewer.org/ NGL Viewer] is offered as a visualization option by the [[wwPDB]]. Its rendering is fast and smooth because it uses [https://developer.mozilla.org/en-US/docs/Web/API/WebGL_API WebGL].
		+	*[https://www.samson-connect.net/ Samson], a powerful visualization and modeling package that is menu-driven. Free for basic use. See demos at [[Sculpting protein conformations]].
	*[[Kinemages, Mage and KiNG]] (KiNG = Kinemage, Next Generation) are designed to present the author's viewpoint of a molecular structure. They excel in specialized areas, but are not optimal for general purpose visualization. KiNG can be used in Proteopedia; an example may be seen at [[Hemoglobin#Hemoglobin_subunit_binding_O2]].		*[[Kinemages, Mage and KiNG]] (KiNG = Kinemage, Next Generation) are designed to present the author's viewpoint of a molecular structure. They excel in specialized areas, but are not optimal for general purpose visualization. KiNG can be used in Proteopedia; an example may be seen at [[Hemoglobin#Hemoglobin_subunit_binding_O2]].
	*[[RasMol]], an open-source stand-alone program released in 1993, and still popular. Effective use of RasMol requires learning a command scripting language.		*[[RasMol]], an open-source stand-alone program released in 1993, and still popular. Effective use of RasMol requires learning a command scripting language.

Eric Martz: /* Free molecular visualization software */

Eric Martz — Mon, 11 Sep 2023 20:34:42 GMT

Free molecular visualization software

←Older revision		Revision as of 20:34, 11 September 2023
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	*[[FirstGlance in Jmol]], an open-source user-interface to [[Jmol]] utilized in the ''3D View'' links in papers in the journal [http://www.nature.com/nature Nature] that report new macromolecular structures. Proteopedia's automatically seeded pages (pages titled with a [[PDB code]]) have links for further exploration of the structure in'' FirstGlance in Jmol''. Although ''FirstGlance in Jmol'' by no means exploits all the power in Jmol, it does show the main structural features of a macromolecule '''without learning any command scripting language'''. [[FirstGlance in Jmol\|More ...]]		*[[FirstGlance in Jmol]], an open-source user-interface to [[Jmol]] utilized in the ''3D View'' links in papers in the journal [http://www.nature.com/nature Nature] that report new macromolecular structures. Proteopedia's automatically seeded pages (pages titled with a [[PDB code]]) have links for further exploration of the structure in'' FirstGlance in Jmol''. Although ''FirstGlance in Jmol'' by no means exploits all the power in Jmol, it does show the main structural features of a macromolecule '''without learning any command scripting language'''. [[FirstGlance in Jmol\|More ...]]
	*[[Chimera]] (free for non-commercial use only).		*[[Chimera]] (free for non-commercial use only).
-	[https://molstar.org/ Mol] (MolStar) is offered as a visualization option by the [[wwPDB]]. ~~Mol*'s~~ rendering is fast and smooth because it uses [https://developer.mozilla.org/en-US/docs/Web/API/WebGL_API WebGL], and it can handle very large numbers of atoms.	+	[https://molstar.org/ Mol] (MolStar) is offered as a visualization option by the [[wwPDB]]. Its rendering is fast and smooth because it uses [https://developer.mozilla.org/en-US/docs/Web/API/WebGL_API WebGL], and it can handle very large numbers of atoms.
		+	*[https://nglviewer.org/ NGL Viewer] is offered as a visualization option by the [[wwPDB]]. Its rendering is fast and smooth because it uses [https://developer.mozilla.org/en-US/docs/Web/API/WebGL_API WebGL].
	*[[Kinemages, Mage and KiNG]] (KiNG = Kinemage, Next Generation) are designed to present the author's viewpoint of a molecular structure. They excel in specialized areas, but are not optimal for general purpose visualization. KiNG can be used in Proteopedia; an example may be seen at [[Hemoglobin#Hemoglobin_subunit_binding_O2]].		*[[Kinemages, Mage and KiNG]] (KiNG = Kinemage, Next Generation) are designed to present the author's viewpoint of a molecular structure. They excel in specialized areas, but are not optimal for general purpose visualization. KiNG can be used in Proteopedia; an example may be seen at [[Hemoglobin#Hemoglobin_subunit_binding_O2]].
	*[[RasMol]], an open-source stand-alone program released in 1993, and still popular. Effective use of RasMol requires learning a command scripting language.		*[[RasMol]], an open-source stand-alone program released in 1993, and still popular. Effective use of RasMol requires learning a command scripting language.

Eric Martz: /* Free molecular visualization software */

Eric Martz — Mon, 11 Sep 2023 20:22:31 GMT

Free molecular visualization software

←Older revision		Revision as of 20:22, 11 September 2023
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	*[[FirstGlance in Jmol]], an open-source user-interface to [[Jmol]] utilized in the ''3D View'' links in papers in the journal [http://www.nature.com/nature Nature] that report new macromolecular structures. Proteopedia's automatically seeded pages (pages titled with a [[PDB code]]) have links for further exploration of the structure in'' FirstGlance in Jmol''. Although ''FirstGlance in Jmol'' by no means exploits all the power in Jmol, it does show the main structural features of a macromolecule '''without learning any command scripting language'''. [[FirstGlance in Jmol\|More ...]]		*[[FirstGlance in Jmol]], an open-source user-interface to [[Jmol]] utilized in the ''3D View'' links in papers in the journal [http://www.nature.com/nature Nature] that report new macromolecular structures. Proteopedia's automatically seeded pages (pages titled with a [[PDB code]]) have links for further exploration of the structure in'' FirstGlance in Jmol''. Although ''FirstGlance in Jmol'' by no means exploits all the power in Jmol, it does show the main structural features of a macromolecule '''without learning any command scripting language'''. [[FirstGlance in Jmol\|More ...]]
	*[[Chimera]] (free for non-commercial use only).		*[[Chimera]] (free for non-commercial use only).
		+	[https://molstar.org/ Mol] (MolStar) is offered as a visualization option by the [[wwPDB]]. Mol*'s rendering is fast and smooth because it uses [https://developer.mozilla.org/en-US/docs/Web/API/WebGL_API WebGL], and it can handle very large numbers of atoms.
	*[[Kinemages, Mage and KiNG]] (KiNG = Kinemage, Next Generation) are designed to present the author's viewpoint of a molecular structure. They excel in specialized areas, but are not optimal for general purpose visualization. KiNG can be used in Proteopedia; an example may be seen at [[Hemoglobin#Hemoglobin_subunit_binding_O2]].		*[[Kinemages, Mage and KiNG]] (KiNG = Kinemage, Next Generation) are designed to present the author's viewpoint of a molecular structure. They excel in specialized areas, but are not optimal for general purpose visualization. KiNG can be used in Proteopedia; an example may be seen at [[Hemoglobin#Hemoglobin_subunit_binding_O2]].
	*[[RasMol]], an open-source stand-alone program released in 1993, and still popular. Effective use of RasMol requires learning a command scripting language.		*[[RasMol]], an open-source stand-alone program released in 1993, and still popular. Effective use of RasMol requires learning a command scripting language.

Joel L. Sussman at 21:25, 7 August 2021

Joel L. Sussman — Sat, 07 Aug 2021 21:25:16 GMT

←Older revision		Revision as of 21:25, 7 August 2021
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	*[[Homology model]]		*[[Homology model]]
	*[[PyMOL]], an open-source molecular visualization program, extremely popular with crystallographers, that requires a subscription fee. Effective use of PyMOL requires that you become familiar with highly abbreviated menus, and/or a command scripting language.		*[[PyMOL]], an open-source molecular visualization program, extremely popular with crystallographers, that requires a subscription fee. Effective use of PyMOL requires that you become familiar with highly abbreviated menus, and/or a command scripting language.
-	*[http://www.weizmann.ac.il/~~ISPC~~/eMovie.html eMovie] is a plugin for PyMOL that facilitates creation of [[Morphs#True_Movies\|true movies]] using a storyboard approach.	+	*[http://www.weizmann.ac.il/old_ISPC/eMovie.html eMovie] is a plugin for PyMOL that facilitates creation of [[Morphs#True_Movies\|true movies]] using a storyboard approach.
	*[[Molecular sculpture]]		*[[Molecular sculpture]]
	*[[Web servers for convenient generation of publication-quality figures for molecular views]]		*[[Web servers for convenient generation of publication-quality figures for molecular views]]

Eric Martz: /* Visualization vs. Modeling */

Eric Martz — Sat, 07 Aug 2021 19:48:26 GMT

Visualization vs. Modeling

←Older revision		Revision as of 19:48, 7 August 2021
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	==Visualization vs. Modeling==		==Visualization vs. Modeling==

-	Software for visualizing the three-dimensional structures of molecules, ''molecular visualization software'', can be distinguished from molecular modeling software. Strictly speaking, ''Visualization'' software displays a pre-existing molecular model without changing it, while ''modeling'' software can create the model, or modify it by adding or removing moieties, changing covalent bonds, bond angles, conformation, or non-covalent interactions.	+	Software for [[Introduction to molecular visualization\|visualizing the three-dimensional structures of molecules]], ''molecular visualization software'', can be distinguished from molecular modeling software. Strictly speaking, ''Visualization'' software displays a pre-existing molecular model without changing it, while ''modeling'' software can create the model, or modify it by adding or removing moieties, changing covalent bonds, bond angles, conformation, or non-covalent interactions.

	==Free molecular visualization software==		==Free molecular visualization software==

Eric Martz: /* Free molecular visualization software */

Eric Martz — Sat, 07 Aug 2021 19:47:04 GMT

Free molecular visualization software

←Older revision		Revision as of 19:47, 7 August 2021
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	*[[Jmol]], an open-source java-based program available in stand-alone or applet forms. The applet is used in Proteopedia, and in the free educational software [[Molecular Workbench]]. Effective use of Jmol requires learning a command scripting language.		*[[Jmol]], an open-source java-based program available in stand-alone or applet forms. The applet is used in Proteopedia, and in the free educational software [[Molecular Workbench]]. Effective use of Jmol requires learning a command scripting language.
	*[[FirstGlance in Jmol]], an open-source user-interface to [[Jmol]] utilized in the ''3D View'' links in papers in the journal [http://www.nature.com/nature Nature] that report new macromolecular structures. Proteopedia's automatically seeded pages (pages titled with a [[PDB code]]) have links for further exploration of the structure in'' FirstGlance in Jmol''. Although ''FirstGlance in Jmol'' by no means exploits all the power in Jmol, it does show the main structural features of a macromolecule '''without learning any command scripting language'''. [[FirstGlance in Jmol\|More ...]]		*[[FirstGlance in Jmol]], an open-source user-interface to [[Jmol]] utilized in the ''3D View'' links in papers in the journal [http://www.nature.com/nature Nature] that report new macromolecular structures. Proteopedia's automatically seeded pages (pages titled with a [[PDB code]]) have links for further exploration of the structure in'' FirstGlance in Jmol''. Although ''FirstGlance in Jmol'' by no means exploits all the power in Jmol, it does show the main structural features of a macromolecule '''without learning any command scripting language'''. [[FirstGlance in Jmol\|More ...]]
		+	*[[Chimera]] (free for non-commercial use only).
	*[[Kinemages, Mage and KiNG]] (KiNG = Kinemage, Next Generation) are designed to present the author's viewpoint of a molecular structure. They excel in specialized areas, but are not optimal for general purpose visualization. KiNG can be used in Proteopedia; an example may be seen at [[Hemoglobin#Hemoglobin_subunit_binding_O2]].		*[[Kinemages, Mage and KiNG]] (KiNG = Kinemage, Next Generation) are designed to present the author's viewpoint of a molecular structure. They excel in specialized areas, but are not optimal for general purpose visualization. KiNG can be used in Proteopedia; an example may be seen at [[Hemoglobin#Hemoglobin_subunit_binding_O2]].
	*[[RasMol]], an open-source stand-alone program released in 1993, and still popular. Effective use of RasMol requires learning a command scripting language.		*[[RasMol]], an open-source stand-alone program released in 1993, and still popular. Effective use of RasMol requires learning a command scripting language.
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	* [http://istar.cse.cuhk.edu.hk/iview/ iView] - an interactive WebGL visualizer of protein-ligand complexes		* [http://istar.cse.cuhk.edu.hk/iview/ iView] - an interactive WebGL visualizer of protein-ligand complexes
	* [https://biasmv.github.io/pv/ PV - JavaScript Protein Viewer]		* [https://biasmv.github.io/pv/ PV - JavaScript Protein Viewer]
-

	==Free molecular modeling software==		==Free molecular modeling software==

Eric Martz: /* See Also */

Eric Martz — Sat, 07 Aug 2021 19:46:13 GMT

Wayne Decatur: add place to put polyview3d

Wayne Decatur — Thu, 11 Feb 2021 16:01:38 GMT

add place to put polyview3d

←Older revision		Revision as of 16:01, 11 February 2021
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	*[http://www.weizmann.ac.il/ISPC/eMovie.html eMovie] is a plugin for PyMOL that facilitates creation of [[Morphs#True_Movies\|true movies]] using a storyboard approach.		*[http://www.weizmann.ac.il/ISPC/eMovie.html eMovie] is a plugin for PyMOL that facilitates creation of [[Morphs#True_Movies\|true movies]] using a storyboard approach.
	*[[Molecular sculpture]]		*[[Molecular sculpture]]
		+	*[[Web servers for convenient generation of publication-quality figures for molecular views]]

←Older revision		Revision as of 19:46, 7 August 2021
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	==See Also==		==See Also==
		+	*[[Introduction to molecular visualization]]
	*[[History of Macromolecular Visualization]]		*[[History of Macromolecular Visualization]]
	*[[Homology model]]		*[[Homology model]]