PyMOL - Revision history

Jaime Prilusky at 15:07, 26 July 2020

2020-07-26T15:07:24Z

←Older revision		Revision as of 15:07, 26 July 2020
Line 19:		Line 19:

	==See Also==		==See Also==
-	*[[~~PyMOL2Jmol Translator~~]]	+	*[[Special:Morph\|Morphing tool]]
	*[http://pymol.org PyMOL.Org], the official download and information home of PyMOL.		*[http://pymol.org PyMOL.Org], the official download and information home of PyMOL.
	*[http://www.weizmann.ac.il/ISPC/eMovie.html eMovie], 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], a plugin for PyMOL that facilitates creation of [[Morphs#True_Movies\|true movies]] using a storyboard approach..

Jaime Prilusky at 17:40, 27 March 2020

2020-03-27T17:40:38Z

←Older revision		Revision as of 17:40, 27 March 2020
Line 1:		Line 1:
	[http://pymol.org PyMOL] is a stand-alone [[Molecular modeling and visualization software\|molecular visualization]] program that is very popular with protein crystallographers because of the high quality of its rendering, its speed and versatility. A large percentage of the figures in journal publications reporting new macromolecular structures are created using PyMOL. PyMOL is the creation of [http://www.delanoscientific.com/ Warren DeLano]. Effective use of PyMOL requires that you become familiar with highly abbreviated menus, and/or a command scripting language.		[http://pymol.org PyMOL] is a stand-alone [[Molecular modeling and visualization software\|molecular visualization]] program that is very popular with protein crystallographers because of the high quality of its rendering, its speed and versatility. A large percentage of the figures in journal publications reporting new macromolecular structures are created using PyMOL. PyMOL is the creation of [http://www.delanoscientific.com/ Warren DeLano]. Effective use of PyMOL requires that you become familiar with highly abbreviated menus, and/or a command scripting language.

-	Molecular scenes prepared in PyMOL can be imported into ~~Protoepedia~~ scenes. [[Jmol]] which Proteopedia, uses for displaying molecular scenes can read a PyMOL session files (.pse file) that you have saved on your computer and convert it directly into a Jmol scene to be saved and displayed in Proteopedia. Specifically, if you open Proteopedia's Scene Authoring Tool, you can click-and-drag the PyMOL session file from your computer's file browser interface into the structure window of the Scene Authoring Tool (on the right). Jmol will then make its '''best attempt''' at reproducing the scene. (Be aware there a few features of PyMOL that are not supported by Jmol. Also, as PyMOL continues to be developed, new fixes in Jmol will likely be needed.) You can then use the Scene Authoring Tool interface to save that scene to Proteopedia in [[Scene authoring tools#'save_scene'_tab\| the typical way]].	+	Molecular scenes prepared in PyMOL can be imported into Proteopedia scenes. [[Jmol]] which Proteopedia, uses for displaying molecular scenes can read a PyMOL session files (.pse file) that you have saved on your computer and convert it directly into a Jmol scene to be saved and displayed in Proteopedia. Specifically, if you open Proteopedia's Scene Authoring Tool, you can click-and-drag the PyMOL session file from your computer's file browser interface into the structure window of the Scene Authoring Tool (on the right). Jmol will then make its '''best attempt''' at reproducing the scene. (Be aware there a few features of PyMOL that are not supported by Jmol. Also, as PyMOL continues to be developed, new fixes in Jmol will likely be needed.) You can then use the Scene Authoring Tool interface to save that scene to Proteopedia in [[Scene authoring tools#'save_scene'_tab\| the typical way]].

	PyMOL has an innovative license: it is open source, but not free in all forms: the author's current ready-to-run downloads (binaries) and up-to-date documentation require payment of modest annual subscription fees. However, a current [http://pymol.org/educational.html free version] is available to students and educators for classroom use, old out-of-date binary builds can be [http://delsci.com/rel/099 freely downloaded] by anyone, and some Linux distributions provide [http://packages.debian.org/stable/pymol PyMOL packages] compiled from the open-source code.		PyMOL has an innovative license: it is open source, but not free in all forms: the author's current ready-to-run downloads (binaries) and up-to-date documentation require payment of modest annual subscription fees. However, a current [http://pymol.org/educational.html free version] is available to students and educators for classroom use, old out-of-date binary builds can be [http://delsci.com/rel/099 freely downloaded] by anyone, and some Linux distributions provide [http://packages.debian.org/stable/pymol PyMOL packages] compiled from the open-source code.

Wayne Decatur: add caveats

2019-09-20T20:33:19Z

add caveats

←Older revision		Revision as of 20:33, 20 September 2019
Line 1:		Line 1:
	[http://pymol.org PyMOL] is a stand-alone [[Molecular modeling and visualization software\|molecular visualization]] program that is very popular with protein crystallographers because of the high quality of its rendering, its speed and versatility. A large percentage of the figures in journal publications reporting new macromolecular structures are created using PyMOL. PyMOL is the creation of [http://www.delanoscientific.com/ Warren DeLano]. Effective use of PyMOL requires that you become familiar with highly abbreviated menus, and/or a command scripting language.		[http://pymol.org PyMOL] is a stand-alone [[Molecular modeling and visualization software\|molecular visualization]] program that is very popular with protein crystallographers because of the high quality of its rendering, its speed and versatility. A large percentage of the figures in journal publications reporting new macromolecular structures are created using PyMOL. PyMOL is the creation of [http://www.delanoscientific.com/ Warren DeLano]. Effective use of PyMOL requires that you become familiar with highly abbreviated menus, and/or a command scripting language.

-	Molecular scenes prepared in PyMOL can be imported into Protoepedia scenes. [[Jmol]] which Proteopedia, uses for displaying molecular scenes can read a PyMOL session files (.pse file) that you have saved on your computer and convert it directly into a Jmol scene to be saved and displayed in Proteopedia. Specifically, if you open Proteopedia's Scene Authoring Tool, you can click-and-drag the PyMOL session file from your computer's file browser interface into the structure window of the Scene Authoring Tool (on the right). Jmol will then make its best attempt at reproducing the scene. You can then use the Scene Authoring Tool interface to save that scene to Proteopedia in [[Scene authoring tools#'save_scene'_tab\| the typical way]].	+	Molecular scenes prepared in PyMOL can be imported into Protoepedia scenes. [[Jmol]] which Proteopedia, uses for displaying molecular scenes can read a PyMOL session files (.pse file) that you have saved on your computer and convert it directly into a Jmol scene to be saved and displayed in Proteopedia. Specifically, if you open Proteopedia's Scene Authoring Tool, you can click-and-drag the PyMOL session file from your computer's file browser interface into the structure window of the Scene Authoring Tool (on the right). Jmol will then make its '''best attempt''' at reproducing the scene. (Be aware there a few features of PyMOL that are not supported by Jmol. Also, as PyMOL continues to be developed, new fixes in Jmol will likely be needed.) You can then use the Scene Authoring Tool interface to save that scene to Proteopedia in [[Scene authoring tools#'save_scene'_tab\| the typical way]].

	PyMOL has an innovative license: it is open source, but not free in all forms: the author's current ready-to-run downloads (binaries) and up-to-date documentation require payment of modest annual subscription fees. However, a current [http://pymol.org/educational.html free version] is available to students and educators for classroom use, old out-of-date binary builds can be [http://delsci.com/rel/099 freely downloaded] by anyone, and some Linux distributions provide [http://packages.debian.org/stable/pymol PyMOL packages] compiled from the open-source code.		PyMOL has an innovative license: it is open source, but not free in all forms: the author's current ready-to-run downloads (binaries) and up-to-date documentation require payment of modest annual subscription fees. However, a current [http://pymol.org/educational.html free version] is available to students and educators for classroom use, old out-of-date binary builds can be [http://delsci.com/rel/099 freely downloaded] by anyone, and some Linux distributions provide [http://packages.debian.org/stable/pymol PyMOL packages] compiled from the open-source code.

Wayne Decatur: fix PyMol capitalization

2019-09-19T18:53:34Z

fix PyMol capitalization

←Older revision		Revision as of 18:53, 19 September 2019
Line 1:		Line 1:
	[http://pymol.org PyMOL] is a stand-alone [[Molecular modeling and visualization software\|molecular visualization]] program that is very popular with protein crystallographers because of the high quality of its rendering, its speed and versatility. A large percentage of the figures in journal publications reporting new macromolecular structures are created using PyMOL. PyMOL is the creation of [http://www.delanoscientific.com/ Warren DeLano]. Effective use of PyMOL requires that you become familiar with highly abbreviated menus, and/or a command scripting language.		[http://pymol.org PyMOL] is a stand-alone [[Molecular modeling and visualization software\|molecular visualization]] program that is very popular with protein crystallographers because of the high quality of its rendering, its speed and versatility. A large percentage of the figures in journal publications reporting new macromolecular structures are created using PyMOL. PyMOL is the creation of [http://www.delanoscientific.com/ Warren DeLano]. Effective use of PyMOL requires that you become familiar with highly abbreviated menus, and/or a command scripting language.

-	Molecular scenes prepared in PyMOL can be imported into Protoepedia scenes. [[Jmol]] which Proteopedia, uses for displaying molecular scenes can read a PyMOL session files (.pse file) that you have saved on your computer and convert it directly into a Jmol scene to be saved and displayed in Proteopedia. Specifically, if you open Proteopedia's Scene Authoring Tool, you can click-and-drag the ~~PyMol~~ session file from your computer's file browser interface into the structure window of the Scene Authoring Tool (on the right). Jmol will then make its best attempt at reproducing the scene. You can then use the Scene Authoring Tool interface to save that scene to Proteopedia in [[Scene authoring tools#'save_scene'_tab\| the typical way]].	+	Molecular scenes prepared in PyMOL can be imported into Protoepedia scenes. [[Jmol]] which Proteopedia, uses for displaying molecular scenes can read a PyMOL session files (.pse file) that you have saved on your computer and convert it directly into a Jmol scene to be saved and displayed in Proteopedia. Specifically, if you open Proteopedia's Scene Authoring Tool, you can click-and-drag the PyMOL session file from your computer's file browser interface into the structure window of the Scene Authoring Tool (on the right). Jmol will then make its best attempt at reproducing the scene. You can then use the Scene Authoring Tool interface to save that scene to Proteopedia in [[Scene authoring tools#'save_scene'_tab\| the typical way]].

	PyMOL has an innovative license: it is open source, but not free in all forms: the author's current ready-to-run downloads (binaries) and up-to-date documentation require payment of modest annual subscription fees. However, a current [http://pymol.org/educational.html free version] is available to students and educators for classroom use, old out-of-date binary builds can be [http://delsci.com/rel/099 freely downloaded] by anyone, and some Linux distributions provide [http://packages.debian.org/stable/pymol PyMOL packages] compiled from the open-source code.		PyMOL has an innovative license: it is open source, but not free in all forms: the author's current ready-to-run downloads (binaries) and up-to-date documentation require payment of modest annual subscription fees. However, a current [http://pymol.org/educational.html free version] is available to students and educators for classroom use, old out-of-date binary builds can be [http://delsci.com/rel/099 freely downloaded] by anyone, and some Linux distributions provide [http://packages.debian.org/stable/pymol PyMOL packages] compiled from the open-source code.

Wayne Decatur: try to fix link

2019-09-19T18:52:45Z

try to fix link

←Older revision		Revision as of 18:52, 19 September 2019
Line 1:		Line 1:
	[http://pymol.org PyMOL] is a stand-alone [[Molecular modeling and visualization software\|molecular visualization]] program that is very popular with protein crystallographers because of the high quality of its rendering, its speed and versatility. A large percentage of the figures in journal publications reporting new macromolecular structures are created using PyMOL. PyMOL is the creation of [http://www.delanoscientific.com/ Warren DeLano]. Effective use of PyMOL requires that you become familiar with highly abbreviated menus, and/or a command scripting language.		[http://pymol.org PyMOL] is a stand-alone [[Molecular modeling and visualization software\|molecular visualization]] program that is very popular with protein crystallographers because of the high quality of its rendering, its speed and versatility. A large percentage of the figures in journal publications reporting new macromolecular structures are created using PyMOL. PyMOL is the creation of [http://www.delanoscientific.com/ Warren DeLano]. Effective use of PyMOL requires that you become familiar with highly abbreviated menus, and/or a command scripting language.

-	Molecular scenes prepared in PyMOL can be imported into Protoepedia scenes. [[Jmol]] which Proteopedia, uses for displaying molecular scenes can read a PyMOL session files (.pse file) that you have saved on your computer and convert it directly into a Jmol scene to be saved and displayed in Proteopedia. Specifically, if you open Proteopedia's Scene Authoring Tool, you can click-and-drag the PyMol session file from your computer's file browser interface into the structure window of the Scene Authoring Tool (on the right). Jmol will then make its best attempt at reproducing the scene. You can then use the Scene Authoring Tool interface to save that scene to Proteopedia in [[Scene authoring tools#'save_scene'_tab the typical way]].	+	Molecular scenes prepared in PyMOL can be imported into Protoepedia scenes. [[Jmol]] which Proteopedia, uses for displaying molecular scenes can read a PyMOL session files (.pse file) that you have saved on your computer and convert it directly into a Jmol scene to be saved and displayed in Proteopedia. Specifically, if you open Proteopedia's Scene Authoring Tool, you can click-and-drag the PyMol session file from your computer's file browser interface into the structure window of the Scene Authoring Tool (on the right). Jmol will then make its best attempt at reproducing the scene. You can then use the Scene Authoring Tool interface to save that scene to Proteopedia in [[Scene authoring tools#'save_scene'_tab\| the typical way]].

	PyMOL has an innovative license: it is open source, but not free in all forms: the author's current ready-to-run downloads (binaries) and up-to-date documentation require payment of modest annual subscription fees. However, a current [http://pymol.org/educational.html free version] is available to students and educators for classroom use, old out-of-date binary builds can be [http://delsci.com/rel/099 freely downloaded] by anyone, and some Linux distributions provide [http://packages.debian.org/stable/pymol PyMOL packages] compiled from the open-source code.		PyMOL has an innovative license: it is open source, but not free in all forms: the author's current ready-to-run downloads (binaries) and up-to-date documentation require payment of modest annual subscription fees. However, a current [http://pymol.org/educational.html free version] is available to students and educators for classroom use, old out-of-date binary builds can be [http://delsci.com/rel/099 freely downloaded] by anyone, and some Linux distributions provide [http://packages.debian.org/stable/pymol PyMOL packages] compiled from the open-source code.

Wayne Decatur: try to fix link

2019-09-19T18:51:55Z

try to fix link

←Older revision		Revision as of 18:51, 19 September 2019
Line 1:		Line 1:
	[http://pymol.org PyMOL] is a stand-alone [[Molecular modeling and visualization software\|molecular visualization]] program that is very popular with protein crystallographers because of the high quality of its rendering, its speed and versatility. A large percentage of the figures in journal publications reporting new macromolecular structures are created using PyMOL. PyMOL is the creation of [http://www.delanoscientific.com/ Warren DeLano]. Effective use of PyMOL requires that you become familiar with highly abbreviated menus, and/or a command scripting language.		[http://pymol.org PyMOL] is a stand-alone [[Molecular modeling and visualization software\|molecular visualization]] program that is very popular with protein crystallographers because of the high quality of its rendering, its speed and versatility. A large percentage of the figures in journal publications reporting new macromolecular structures are created using PyMOL. PyMOL is the creation of [http://www.delanoscientific.com/ Warren DeLano]. Effective use of PyMOL requires that you become familiar with highly abbreviated menus, and/or a command scripting language.

-	Molecular scenes prepared in PyMOL can be imported into Protoepedia scenes. [[Jmol]] which Proteopedia, uses for displaying molecular scenes can read a PyMOL session files (.pse file) that you have saved on your computer and convert it directly into a Jmol scene to be saved and displayed in Proteopedia. Specifically, if you open Proteopedia's Scene Authoring Tool, you can click-and-drag the PyMol session file from your computer's file browser interface into the structure window of the Scene Authoring Tool (on the right). Jmol will then make its best attempt at reproducing the scene. You can then use the Scene Authoring Tool interface to save that scene to Proteopedia in [[Scene authoring tools#~~.27save_scene.27_tab~~ the typical way]].	+	Molecular scenes prepared in PyMOL can be imported into Protoepedia scenes. [[Jmol]] which Proteopedia, uses for displaying molecular scenes can read a PyMOL session files (.pse file) that you have saved on your computer and convert it directly into a Jmol scene to be saved and displayed in Proteopedia. Specifically, if you open Proteopedia's Scene Authoring Tool, you can click-and-drag the PyMol session file from your computer's file browser interface into the structure window of the Scene Authoring Tool (on the right). Jmol will then make its best attempt at reproducing the scene. You can then use the Scene Authoring Tool interface to save that scene to Proteopedia in [[Scene authoring tools#'save_scene'_tab the typical way]].

	PyMOL has an innovative license: it is open source, but not free in all forms: the author's current ready-to-run downloads (binaries) and up-to-date documentation require payment of modest annual subscription fees. However, a current [http://pymol.org/educational.html free version] is available to students and educators for classroom use, old out-of-date binary builds can be [http://delsci.com/rel/099 freely downloaded] by anyone, and some Linux distributions provide [http://packages.debian.org/stable/pymol PyMOL packages] compiled from the open-source code.		PyMOL has an innovative license: it is open source, but not free in all forms: the author's current ready-to-run downloads (binaries) and up-to-date documentation require payment of modest annual subscription fees. However, a current [http://pymol.org/educational.html free version] is available to students and educators for classroom use, old out-of-date binary builds can be [http://delsci.com/rel/099 freely downloaded] by anyone, and some Linux distributions provide [http://packages.debian.org/stable/pymol PyMOL packages] compiled from the open-source code.

Wayne Decatur: update Pymol to Jmol to Proteopedia Scene steps

2019-09-19T18:50:45Z

update Pymol to Jmol to Proteopedia Scene steps

←Older revision		Revision as of 18:50, 19 September 2019
Line 1:		Line 1:
	[http://pymol.org PyMOL] is a stand-alone [[Molecular modeling and visualization software\|molecular visualization]] program that is very popular with protein crystallographers because of the high quality of its rendering, its speed and versatility. A large percentage of the figures in journal publications reporting new macromolecular structures are created using PyMOL. PyMOL is the creation of [http://www.delanoscientific.com/ Warren DeLano]. Effective use of PyMOL requires that you become familiar with highly abbreviated menus, and/or a command scripting language.		[http://pymol.org PyMOL] is a stand-alone [[Molecular modeling and visualization software\|molecular visualization]] program that is very popular with protein crystallographers because of the high quality of its rendering, its speed and versatility. A large percentage of the figures in journal publications reporting new macromolecular structures are created using PyMOL. PyMOL is the creation of [http://www.delanoscientific.com/ Warren DeLano]. Effective use of PyMOL requires that you become familiar with highly abbreviated menus, and/or a command scripting language.

-	Molecular scenes prepared in PyMOL can be imported into Protoepedia scenes~~, using the~~ [[~~PyMOL2Jmol_Translator~~]] ~~(not yet released),~~ which ~~allows you to choose~~ a PyMOL session ~~file~~ (.pse file) that you have saved on your computer and ~~have~~ it ~~converted~~ directly into a Jmol scene to be saved and displayed in Proteopedia.	+	Molecular scenes prepared in PyMOL can be imported into Protoepedia scenes. [[Jmol]] which Proteopedia, uses for displaying molecular scenes can read a PyMOL session files (.pse file) that you have saved on your computer and convert it directly into a Jmol scene to be saved and displayed in Proteopedia. Specifically, if you open Proteopedia's Scene Authoring Tool, you can click-and-drag the PyMol session file from your computer's file browser interface into the structure window of the Scene Authoring Tool (on the right). Jmol will then make its best attempt at reproducing the scene. You can then use the Scene Authoring Tool interface to save that scene to Proteopedia in [[Scene authoring tools#.27save_scene.27_tab the typical way]].

	PyMOL has an innovative license: it is open source, but not free in all forms: the author's current ready-to-run downloads (binaries) and up-to-date documentation require payment of modest annual subscription fees. However, a current [http://pymol.org/educational.html free version] is available to students and educators for classroom use, old out-of-date binary builds can be [http://delsci.com/rel/099 freely downloaded] by anyone, and some Linux distributions provide [http://packages.debian.org/stable/pymol PyMOL packages] compiled from the open-source code.		PyMOL has an innovative license: it is open source, but not free in all forms: the author's current ready-to-run downloads (binaries) and up-to-date documentation require payment of modest annual subscription fees. However, a current [http://pymol.org/educational.html free version] is available to students and educators for classroom use, old out-of-date binary builds can be [http://delsci.com/rel/099 freely downloaded] by anyone, and some Linux distributions provide [http://packages.debian.org/stable/pymol PyMOL packages] compiled from the open-source code.

Eric Martz: /* See Also */

2016-02-06T21:21:34Z

Eric Martz: /* See Also */

2011-07-22T19:02:29Z

Eric Martz: /* See Also */

2011-07-22T19:00:22Z

←Older revision		Revision as of 21:21, 6 February 2016
Line 23:		Line 23:
	*[http://www.weizmann.ac.il/ISPC/eMovie.html eMovie], 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], a plugin for PyMOL that facilitates creation of [[Morphs#True_Movies\|true movies]] using a storyboard approach..
	*[[Molecular modeling and visualization software]]		*[[Molecular modeling and visualization software]]
-	*[http://molvisindex.org World Index of Molecular Visualization Software]

	==References and Notes==		==References and Notes==
	<references />		<references />

←Older revision		Revision as of 19:02, 22 July 2011
Line 21:		Line 21:
	*[[PyMOL2Jmol Translator]]		*[[PyMOL2Jmol Translator]]
	*[http://pymol.org PyMOL.Org], the official download and information home of PyMOL.		*[http://pymol.org PyMOL.Org], the official download and information home of PyMOL.
-	*[http://www.weizmann.ac.il/ISPC/eMovie.html eMovie], a ~~storyboard-based tool~~ for ~~making molecular~~ movies using ~~PyMOL~~.	+	*[http://www.weizmann.ac.il/ISPC/eMovie.html eMovie], a plugin for PyMOL that facilitates creation of [[Morphs#True_Movies\|true movies]] using a storyboard approach..
	*[[Molecular modeling and visualization software]]		*[[Molecular modeling and visualization software]]
	*[http://molvisindex.org World Index of Molecular Visualization Software]		*[http://molvisindex.org World Index of Molecular Visualization Software]

←Older revision		Revision as of 19:00, 22 July 2011
Line 21:		Line 21:
	*[[PyMOL2Jmol Translator]]		*[[PyMOL2Jmol Translator]]
	*[http://pymol.org PyMOL.Org], the official download and information home of PyMOL.		*[http://pymol.org PyMOL.Org], the official download and information home of PyMOL.
		+	*[http://www.weizmann.ac.il/ISPC/eMovie.html eMovie], a storyboard-based tool for making molecular movies using PyMOL.
	*[[Molecular modeling and visualization software]]		*[[Molecular modeling and visualization software]]
	*[http://molvisindex.org World Index of Molecular Visualization Software]		*[http://molvisindex.org World Index of Molecular Visualization Software]