User:Wayne Decatur/SandboxTeachingInfo - Revision history

Wayne Decatur: /* Other student projects and teaching resources in Proteopedia */

2009-05-22T19:14:16Z

Other student projects and teaching resources in Proteopedia

← Older revision		Revision as of 19:14, 22 May 2009
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	*[[Teaching Strategies Using Proteopedia]]		*[[Teaching Strategies Using Proteopedia]]
	*[[Teaching Scenes, Tutorials, and Educators%27 Pages]]		*[[Teaching Scenes, Tutorials, and Educators%27 Pages]]
			*[[User:Jaime Prilusky/Sandbox quiz \|Quizzes with Proteopedia]]

Wayne Decatur at 23:21, 24 November 2008

2008-11-24T23:21:43Z

← Older revision		Revision as of 23:21, 24 November 2008
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	*[http://www.bioinformatics.org/jmol-tutorials/jtat/_docs/jtatdocs.htm#fgijscripting Scripting in FirstGlance in Jmol directions as found a Jmol Tutorial Authoring Tools (JTAT)] also has more information on going from scenes generated in FirstGlance in Jmol to a state script and this approach can be adapted to going from FirstGlance in Jmol scenes to Proteopedia scenes, the important point being to be use consistent version of Jmol.		*[http://www.bioinformatics.org/jmol-tutorials/jtat/_docs/jtatdocs.htm#fgijscripting Scripting in FirstGlance in Jmol directions as found a Jmol Tutorial Authoring Tools (JTAT)] also has more information on going from scenes generated in FirstGlance in Jmol to a state script and this approach can be adapted to going from FirstGlance in Jmol scenes to Proteopedia scenes, the important point being to be use consistent version of Jmol.
	*[http://chemapps.stolaf.edu/pe/protexpl/ Jmol Protein Explorer's] powerful Quickviews approach really helps quickly generate particular scenes or ideas for scenes to generate elsewhere. Using the information detailed at the JTAT site on extracting state scripts, it is possible to go from these views to Proteopedia scenes; however, as the version of Jmol differs there may be slight discrepancies.		*[http://chemapps.stolaf.edu/pe/protexpl/ Jmol Protein Explorer's] powerful Quickviews approach really helps quickly generate particular scenes or ideas for scenes to generate elsewhere. Using the information detailed at the JTAT site on extracting state scripts, it is possible to go from these views to Proteopedia scenes; however, as the version of Jmol differs there may be slight discrepancies.
	'''Be prepared to do some troubleshooting to get the exact scene you need.''' Keep in mind this an evolving and improving system and that some means of generating aspects of scenes outside of Proteopedia's Scene authoring tools might not be saved in the scene information properly by Proteopedia's Scene Authoring Tools. I have found this to be the case with instances involving representations that use '~~surfaces~~', 'dots', and 'configuration' settings. For the problematic instances I mention, I found that troubleshooting simply involved either using a state script or Proteopedia's own Scene Authoring Tools to get close to the scene I want and then using the Jmol console to execute the problematic commands bypasses the errors I was encountering.		'''Be prepared to do some troubleshooting to get the exact scene you need.''' Keep in mind this an evolving and improving system and that some means of generating aspects of scenes outside of Proteopedia's Scene authoring tools might not be saved in the scene information properly by Proteopedia's Scene Authoring Tools. I have found this to be the case with instances involving representations that use 'isosurface', 'dots', and 'configuration' settings. For the problematic instances I mention, I found that troubleshooting simply involved either using a state script or Proteopedia's own Scene Authoring Tools to get close to the scene I want and then using the Jmol console to execute the problematic commands bypasses the errors I was encountering.
	<br>		<br>
	'''SAVE OFTEN!'''<br>		'''SAVE OFTEN!'''<br>

Wayne Decatur at 20:32, 24 November 2008

2008-11-24T20:32:25Z

← Older revision		Revision as of 20:32, 24 November 2008
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	===Authoring scenes within pages===		===Authoring scenes within pages===
	*[[Scene authoring tools\|Molecular Scene Authoring Tools]]		*[[Scene authoring tools\|Molecular Scene Authoring Tools]]
			*[[User:Wayne Decatur/SandboxTransitionExample\|Example of scenes without and with transitions]]
	*[[User:Tom Gluick/glutamine synthetase]] (University of Maryland, Baltimore County). Includes instructions for using Jmol commands in the Jmol console for advanced scene authoring.		*[[User:Tom Gluick/glutamine synthetase]] (University of Maryland, Baltimore County). Includes instructions for using Jmol commands in the Jmol console for advanced scene authoring.
	===Advanced Scene Authoring===		===Advanced Scene Authoring===

Wayne Decatur at 10:16, 21 November 2008

2008-11-21T10:16:12Z

← Older revision		Revision as of 10:16, 21 November 2008
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	*[[User:Wayne Decatur/Plant Viral Protein p19 Suppression of RNA Silencing]] is another example of a protected user subpage.		*[[User:Wayne Decatur/Plant Viral Protein p19 Suppression of RNA Silencing]] is another example of a protected user subpage.
	*[[Help:Protected Pages]] tells how to create protected subpages of your user page.		*[[Help:Protected Pages]] tells how to create protected subpages of your user page.
			*[[Teaching Strategies Using Proteopedia]] describes using temporary sandbox pages for practice or experimenting or colloboration.
	===Authoring pages===		===Authoring pages===
	*[[Proteopedia:Video Guide\|Movies Showing How to Author Proteopedia Pages]]		*[[Proteopedia:Video Guide\|Movies Showing How to Author Proteopedia Pages]]

Wayne Decatur at 10:08, 21 November 2008

2008-11-21T10:08:32Z

← Older revision		Revision as of 10:08, 21 November 2008
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	===Other student projects and teaching resources in Proteopedia===		===Other student projects and teaching resources in Proteopedia===
	*[[Student Projects]]		*[[Student Projects]]
			*[[Teaching Strategies Using Proteopedia]]
	*[[Teaching Scenes, Tutorials, and Educators%27 Pages]]		*[[Teaching Scenes, Tutorials, and Educators%27 Pages]]

Wayne Decatur at 08:47, 21 November 2008

2008-11-21T08:47:06Z

← Older revision		Revision as of 08:47, 21 November 2008
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	*[http://molvis.sdsc.edu/fgij/fg.htm?mol=1RPU FirstGlance in Jmol]		*[http://molvis.sdsc.edu/fgij/fg.htm?mol=1RPU FirstGlance in Jmol]
	*[[Lac repressor\|Lac repressor at Proteopedia]]		*[[Lac repressor\|Lac repressor at Proteopedia]]
			*''Proteopedia - a scientific 'wiki' bridging the rift between 3D structure and function of biomacromolecules'', Eran Hodis, Jaime Prilusky, Eric Martz, Israel Silman, John Moult and Joel L Sussman. [http://genomebiology.com/2008/9/8/R121 ''Genome Biology'' 9:R121, August 2008] or [http://dx.doi.org/10.1186/gb-2008-9-8-r121 doi:10.1186/gb-2008-9-8-r121]
	===Types of pages===		===Types of pages===
	*[[Proteopedia:Topic Pages]]		*[[Proteopedia:Topic Pages]]

Wayne Decatur at 08:38, 21 November 2008

2008-11-21T08:38:04Z

← Older revision		Revision as of 08:38, 21 November 2008
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	*[[Proteopedia:Topic Pages]]		*[[Proteopedia:Topic Pages]]
	*[[Lac repressor\|Lac repressor at Proteopedia]] is an example of a topic page.		*[[Lac repressor\|Lac repressor at Proteopedia]] is an example of a topic page.
	*[[http://proteopedia.org/wiki/VideoGuide/ProteopediaVideoGuide3/ProteopediaVideoGuide3.htm\|Video on seeded vs. topic pages at Proteopedia]]		*[http://proteopedia.org/wiki/VideoGuide/ProteopediaVideoGuide3/ProteopediaVideoGuide3.htm\|Video on seeded vs. topic pages at Proteopedia]
	*[[1rpu]] is a seeded page.		*[[1rpu]] is a seeded page.
	*[[1eve]] is a seeded page that had been expanded.		*[[1eve]] is a seeded page that had been expanded.

Wayne Decatur at 05:44, 21 November 2008

2008-11-21T05:44:29Z

← Older revision		Revision as of 05:44, 21 November 2008
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	*[[User:Eric Martz/Nucleosomes]] is a protected page that is a subpage of a user. It is authored by that user and only editable by that user.		*[[User:Eric Martz/Nucleosomes]] is a protected page that is a subpage of a user. It is authored by that user and only editable by that user.
	*[[User:Wayne Decatur]]		*[[User:Wayne Decatur]]
	*[[User:Wayne Decatur/Plant Viral Protein p19 Suppression of RNA Silencing]] is another example if a protected user subpage.		*[[User:Wayne Decatur/Plant Viral Protein p19 Suppression of RNA Silencing]] is another example of a protected user subpage.
	*[[Help:Protected Pages]] tells how to create protected subpages of your user page.		*[[Help:Protected Pages]] tells how to create protected subpages of your user page.
	===Authoring pages===		===Authoring pages===

Wayne Decatur at 01:36, 21 November 2008

2008-11-21T01:36:52Z

← Older revision		Revision as of 01:36, 21 November 2008
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	*[http://chemapps.stolaf.edu/jmol/docs/ Jmol interactive scripting documentation]		*[http://chemapps.stolaf.edu/jmol/docs/ Jmol interactive scripting documentation]
	*[http://jmol.sourceforge.net/docs/ Jmol documentation, features illustrated and detailed surface options]		*[http://jmol.sourceforge.net/docs/ Jmol documentation, features illustrated and detailed surface options]
	===Other student projects and ~~teachig~~ resources in Proteopedia===		===Other student projects and teaching resources in Proteopedia===
			*[[Student Projects]]
	*[[Teaching Scenes, Tutorials, and Educators%27 Pages]]		*[[Teaching Scenes, Tutorials, and Educators%27 Pages]]
	*[[Student Projects]]

Wayne Decatur at 01:36, 21 November 2008

2008-11-21T01:36:08Z

← Older revision		Revision as of 01:36, 21 November 2008
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	*[[User:Wayne Decatur]]		*[[User:Wayne Decatur]]
	*[[User:Wayne Decatur/Plant Viral Protein p19 Suppression of RNA Silencing]] is another example if a protected user subpage.		*[[User:Wayne Decatur/Plant Viral Protein p19 Suppression of RNA Silencing]] is another example if a protected user subpage.
	*[[Help:Protected Pages]] tells how to create protected as subpages of your user page.		*[[Help:Protected Pages]] tells how to create protected subpages of your user page.
	===Authoring pages===		===Authoring pages===
	*[[Proteopedia:Video Guide\|Movies Showing How to Author Proteopedia Pages]]		*[[Proteopedia:Video Guide\|Movies Showing How to Author Proteopedia Pages]]
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	*[http://www.bioinformatics.org/jmol-tutorials/jtat/_docs/jtatdocs.htm#fgijscripting Scripting in FirstGlance in Jmol directions as found a Jmol Tutorial Authoring Tools (JTAT)] also has more information on going from scenes generated in FirstGlance in Jmol to a state script and this approach can be adapted to going from FirstGlance in Jmol scenes to Proteopedia scenes, the important point being to be use consistent version of Jmol.		*[http://www.bioinformatics.org/jmol-tutorials/jtat/_docs/jtatdocs.htm#fgijscripting Scripting in FirstGlance in Jmol directions as found a Jmol Tutorial Authoring Tools (JTAT)] also has more information on going from scenes generated in FirstGlance in Jmol to a state script and this approach can be adapted to going from FirstGlance in Jmol scenes to Proteopedia scenes, the important point being to be use consistent version of Jmol.
	*[http://chemapps.stolaf.edu/pe/protexpl/ Jmol Protein Explorer's] powerful Quickviews approach really helps quickly generate particular scenes or ideas for scenes to generate elsewhere. Using the information detailed at the JTAT site on extracting state scripts, it is possible to go from these views to Proteopedia scenes; however, as the version of Jmol differs there may be slight discrepancies.		*[http://chemapps.stolaf.edu/pe/protexpl/ Jmol Protein Explorer's] powerful Quickviews approach really helps quickly generate particular scenes or ideas for scenes to generate elsewhere. Using the information detailed at the JTAT site on extracting state scripts, it is possible to go from these views to Proteopedia scenes; however, as the version of Jmol differs there may be slight discrepancies.
	'''Be prepared to do some troubleshooting to get the exact scene you need.''' Keep in mind this an evolving and improving system and that some means of generating aspects of scenes outside of Proteopedia's Scene authoring tools might not be saved in the scene information properly by Proteopedia's Scene Authoring Tools. I have found this to be the case with instances involving representations that use 'surfaces', 'dots', and 'configuration' settings. For the problematic ~~instance~~ I mention, I found that troubleshooting simply involved either using a state script or Proteopedia's own Scene Authoring Tools to get close to the scene I want and then using the Jmol console to execute the problematic commands bypasses the errors I was encountering.		'''Be prepared to do some troubleshooting to get the exact scene you need.''' Keep in mind this an evolving and improving system and that some means of generating aspects of scenes outside of Proteopedia's Scene authoring tools might not be saved in the scene information properly by Proteopedia's Scene Authoring Tools. I have found this to be the case with instances involving representations that use 'surfaces', 'dots', and 'configuration' settings. For the problematic instances I mention, I found that troubleshooting simply involved either using a state script or Proteopedia's own Scene Authoring Tools to get close to the scene I want and then using the Jmol console to execute the problematic commands bypasses the errors I was encountering.
	<br>		<br>
	'''SAVE OFTEN!'''<br>		'''SAVE OFTEN!'''<br>