Jmol in the Classroom - Revision history

EricMartz at 21:50, 3 January 2021

2021-01-03T21:50:43Z

EricMartz at 21:50, 3 January 2021

2021-01-03T21:50:07Z

EricMartz at 21:49, 3 January 2021

2021-01-03T21:49:33Z

EricMartz at 21:43, 3 January 2021

2021-01-03T21:43:36Z

EricMartz at 21:37, 3 January 2021

2021-01-03T21:37:51Z

AngelHerraez: fixing wrong characters due to change in charset during migration of the wiki; text recovered from the old server

2019-03-25T23:02:22Z

fixing wrong characters due to change in charset during migration of the wiki; text recovered from the old server

BLachner at 12:04, 2 April 2013

2013-04-02T12:04:49Z

AngelHerraez: Integrating Jmol in virtual learning environments

2011-06-30T13:49:30Z

Integrating Jmol in virtual learning environments

AngelHerraez: fix link

2011-06-30T13:08:50Z

fix link

AngelHerraez: Jmol in Blackboard

2011-06-30T13:04:54Z

Jmol in Blackboard

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 ==Proteopedia.Org==
-[http://proteopedia.org Proteopedia.Org] is a protein structure wiki that makes it easy to create customized molecular scenes. While reading about the molecule, you click '''green links''' that change the interactive 3D molecular scene in JSmol.
+[http://proteopedia.org Proteopedia.Org] is a JSmol-based protein structure wiki that makes it easy to create customized molecular scenes. While reading about the molecule, you click '''green links''' that change the interactive 3D molecular scene in JSmol.
 * [http://proteopedia.org/wiki/index.php/Teaching_Strategies_Using_Proteopedia Teaching Strategies Using Proteopedia]. Proteopedia is widely used by educators.

@@ Line 7: / Line 7: @@
 ==Proteopedia.Org==
-[http://proteopedia.org Proteopedia.Org] is a protein structure wiki that makes it easy to create customized molecular scenes. While reading about the molecule, you click '''{{Font color|green|green links}}''' that change the interactive 3D molecular scene in JSmol.
+[http://proteopedia.org Proteopedia.Org] is a protein structure wiki that makes it easy to create customized molecular scenes. While reading about the molecule, you click '''green links''' that change the interactive 3D molecular scene in JSmol.
 * [http://proteopedia.org/wiki/index.php/Teaching_Strategies_Using_Proteopedia Teaching Strategies Using Proteopedia]. Proteopedia is widely used by educators.

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 *To find it, google ''firstglance'' as a single word, no space.
 *Lesson plans with syllabi and assessments for students at various levels, using FirstGlance: [http://proteopedia.org/wiki/index.php/User:Eric_Martz/Introduction_to_Structural_Bioinformatics Introduction to Structural Bioinformatics].
 == Functional Groups: getting structures by name ==

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 ==FirstGlance in Jmol==
 *[http://FirstGlance.Jmol.Org FirstGlance in Jmol] offers a guided tour of any macromolecule (PDB code or uploaded model). Information in the PDB file header is presented in readable form with links to extensive help. Technical language is minimized; for example, "Reliability" offers an objective assessment of free-R (e. g. "Better than average at this resolution") with explanations in minimally-technical language. Secondary structure, hydrophobic cores, charge distribution, "local uncertainty" (B factor/temperature factor) are available at a single click. Find any residue or sequence motif in the 3D structure. Find the non-covalent interactions with any moiety. You don't need to learn any Jmol commands. Used more than 1,000,000 times. Suitable for high school up to investigators in biochemical research teams. [https://proteopedia.org/wiki/fgij/whatis.htm More].
 == Functional Groups: getting structures by name ==

← Older revision		Revision as of 21:37, 3 January 2021
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	''The idea behind this page is that you enter "teachable moments" when you have used Jmol in an effective way during class.''		''The idea behind this page is that you enter "teachable moments" when you have used Jmol in an effective way during class.''
		+
		+	==FirstGlance in Jmol==
		+	*[http://FirstGlance.Jmol.Org FirstGlance in Jmol] offers a guided tour of any macromolecule (PDB code or uploaded model). Information in the PDB file header is presented in readable form with links to extensive help. Technical language is minimized; for example, "Reliability" offers an objective assessment of free-R (e. g. "Better than average at this resolution") with explanations in minimally-technical language. Secondary structure, hydrophobic cores, charge distribution, "local uncertainty" (B factor/temperature factor) are available at a single click. Find any residue or sequence motif in the 3D structure. Find the non-covalent interactions with any moiety. You don't need to learn any Jmol commands. Used more than 1,000,000 times. Suitable for high school up to investigators in biochemical research teams. [https://proteopedia.org/wiki/fgij/whatis.htm More].

	== Functional Groups: getting structures by name ==		== Functional Groups: getting structures by name ==

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 This page has a button on the right that uses the <code>prompt</code> command and taps into the NIH CACTUS service using <code>load $</code>''chemicalName'' (Jmol 12.1).
-I just clicked on "Load MOL by NAME" and then asked the students to give me a name of something they knew, like a medication.Â
+I just clicked on "Load MOL by NAME" and then asked the students to give me a name of something they knew, like a medication.
-We ended up looking at diphenylhydramine, morphine, THC, heroin, hydrocodone, adderall, and tetracycline, writing out several of these structures on the board based on the 3D models. This lead to discussions of reactivity, hints about the connections between names (even these trade names) and functional groups, a little about the blood/brain barrier issue, hints about synthesis (it's amazing how simple many of these drugs are).Â
+We ended up looking at diphenylhydramine, morphine, THC, heroin, hydrocodone, adderall, and tetracycline, writing out several of these structures on the board based on the 3D models. This lead to discussions of reactivity, hints about the connections between names (even these trade names) and functional groups, a little about the blood/brain barrier issue, hints about synthesis (it's amazing how simple many of these drugs are).
 Great fun!
@@ Line 22: / Line 22: @@
 == Jmol in Wiki ==
-I use the Wiki-Extension to show molecules in a Wiki that is hosted by the german ZUM (Zentrale fÃ¼r Unterrichts-Medien = Central for Teaching with Media).
+I use the Wiki-Extension to show molecules in a Wiki that is hosted by the german ZUM (Zentrale für Unterrichts-Medien = Central for Teaching with Media).
 Example: http://wikis.zum.de/chemie-digital/Frau_Lachner/Fette
 --[[User:BLachner|BLachner]] 14:04, 2 April 2013 (CEST)

← Older revision		Revision as of 12:04, 2 April 2013
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	[http://telstar.ote.cmu.edu/biology/papers/ Molecular visualization in STEM education: Leveraging Jmol in an integrated assessment platform]. G. Rule, D. Bajzek & A. Kessler (2010), in J. Sanchez & K. Zhang (eds.), ''Proceedings of World Conference on E-Learning in Corporate, Government, Healthcare, and Higher Education 2010'', pp. 304-309. Chesapeake, VA: AACE.		[http://telstar.ote.cmu.edu/biology/papers/ Molecular visualization in STEM education: Leveraging Jmol in an integrated assessment platform]. G. Rule, D. Bajzek & A. Kessler (2010), in J. Sanchez & K. Zhang (eds.), ''Proceedings of World Conference on E-Learning in Corporate, Government, Healthcare, and Higher Education 2010'', pp. 304-309. Chesapeake, VA: AACE.
		+
		+
		+	== Jmol in Wiki ==
		+
		+	I use the Wiki-Extension to show molecules in a Wiki that is hosted by the german ZUM (Zentrale fÃ¼r Unterrichts-Medien = Central for Teaching with Media).
		+
		+	Example: http://wikis.zum.de/chemie-digital/Frau_Lachner/Fette
		+
		+	--[[User:BLachner\|BLachner]] 14:04, 2 April 2013 (CEST)

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 Great fun!
-== Integrating Jmol in Blackboard&trade; virtual learning environment ==
+== Integrating Jmol in virtual learning environments ==
 [http://www.elearning.eps.manchester.ac.uk/wp-content/uploads/2011/05/Symposium_Publication.pdf#page=12 Using Java applets to enhance online teaching and assessment in Blackboard]. Tim Wallace (2011), in ''Symposium on the Benefits of eLearning Technologies''. University of Manchester.

← Older revision		Revision as of 13:08, 30 June 2011
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	== Integrating Jmol in Blackboard™ virtual learning environment ==		== Integrating Jmol in Blackboard™ virtual learning environment ==
−	[http://www.elearning.eps.manchester.ac.uk/wp-content/uploads/2011/05/Symposium_Publication.pdf?page=12 Using Java applets to enhance online teaching and assessment in Blackboard]. Tim Wallace (2011), in ''Symposium on the Benefits of eLearning Technologies''. University of Manchester.	+	[http://www.elearning.eps.manchester.ac.uk/wp-content/uploads/2011/05/Symposium_Publication.pdf#page=12 Using Java applets to enhance online teaching and assessment in Blackboard]. Tim Wallace (2011), in ''Symposium on the Benefits of eLearning Technologies''. University of Manchester.

← Older revision		Revision as of 13:04, 30 June 2011
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	Great fun!		Great fun!
		+
		+	== Integrating Jmol in Blackboard™ virtual learning environment ==
		+	[http://www.elearning.eps.manchester.ac.uk/wp-content/uploads/2011/05/Symposium_Publication.pdf?page=12 Using Java applets to enhance online teaching and assessment in Blackboard]. Tim Wallace (2011), in ''Symposium on the Benefits of eLearning Technologies''. University of Manchester.