Example BioMolViz Assessment - Revision history

Karsten Theis at 17:10, 10 February 2021

2021-02-10T17:10:23Z

← Older revision		Revision as of 17:10, 10 February 2021
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	''Clicking on any of the green links in the following paragraph will show an example of how the learner's model may look at that stage of the process''		''Clicking on any of the green links in the following paragraph will show an example of how the learner's model may look at that stage of the process''

	To show mastery, the learner will first focus on <scene name='86/865933/Unit_a/5'>subunit A of the complex</scene>, hiding subunit B for clarity. An <scene name='87/870565/Zoom_ligand_spacefill/1'>unobscured view of the ligand</scene> is obtained by rotating the macromolecule and zooming in. To display interactions, the learner will first replace the spacefilling representation of the ligand with a <scene name='86/865933/Zoom_ligand_stick/2'>stick representation</scene>. To view the interacting residues, the learner shows amino acid residues within 5Å of the active site <scene name='86/865933/Zoom_ligand_plus_as_stick/3'>as sticks and displays them with CPK coloring</scene>. For contrast, the learner colors the ligand magenta. In this view, water molecules within 5Å of the ligand are displayed as well. The view has gotten busy, so to focus in on the active site residues, the learner can <scene name='86/865933/As_no_cartoon/1'>hide the cartoon rendering of the protein</scene>, and then show the <scene name='86/865933/As_no_cartoon_with_labels/1'>active site residues with labels</scene>. The learner then executes a command to <scene name='86/865933/As_no_cartoon_labels_hbonds/1'>show hydrogen bonds</scene> within the active site, including those to the ligand, or measures polar contacts manually.		To show mastery, the learner will first focus on <scene name='86/865933/Unit_a/5'>subunit A of the complex</scene>, hiding subunit B for clarity. An <scene name='87/870565/Zoom_ligand_spacefill/2'>unobscured view of the ligand</scene> is obtained by rotating the macromolecule and zooming in. To display interactions, the learner will first replace the spacefilling representation of the ligand with a <scene name='86/865933/Zoom_ligand_stick/2'>stick representation</scene>. To view the interacting residues, the learner shows amino acid residues within 5Å of the active site <scene name='86/865933/Zoom_ligand_plus_as_stick/3'>as sticks and displays them with CPK coloring</scene>. For contrast, the learner colors the ligand magenta. In this view, water molecules within 5Å of the ligand are displayed as well. The view has gotten busy, so to focus in on the active site residues, the learner can <scene name='86/865933/As_no_cartoon/1'>hide the cartoon rendering of the protein</scene>, and then show the <scene name='86/865933/As_no_cartoon_with_labels/1'>active site residues with labels</scene>. The learner then executes a command to <scene name='86/865933/As_no_cartoon_labels_hbonds/1'>show hydrogen bonds</scene> within the active site, including those to the ligand, or measures polar contacts manually.

	</StructureSection>		</StructureSection>

Karsten Theis at 17:08, 10 February 2021

2021-02-10T17:08:07Z

← Older revision		Revision as of 17:08, 10 February 2021
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	''Clicking on any of the green links in the following paragraph will show an example of how the learner's model may look at that stage of the process''		''Clicking on any of the green links in the following paragraph will show an example of how the learner's model may look at that stage of the process''

	To show mastery, the learner will first focus on <scene name='86/865933/Unit_a/5'>subunit A of the complex</scene>, hiding subunit B for clarity. An <scene name='86/~~865933~~/Zoom_ligand_spacefill/4'>unobscured view of the ligand</scene> is obtained by rotating the macromolecule and zooming in. To display interactions, the learner will first replace the spacefilling representation of the ligand with a <scene name='86/865933/Zoom_ligand_stick/2'>stick representation</scene>. To view the interacting residues, the learner shows amino acid residues within 5Å of the active site <scene name='86/865933/Zoom_ligand_plus_as_stick/3'>as sticks and displays them with CPK coloring</scene>. For contrast, the learner colors the ligand magenta. In this view, water molecules within 5Å of the ligand are displayed as well. The view has gotten busy, so to focus in on the active site residues, the learner can <scene name='86/865933/As_no_cartoon/1'>hide the cartoon rendering of the protein</scene>, and then show the <scene name='86/865933/As_no_cartoon_with_labels/1'>active site residues with labels</scene>. The learner then executes a command to <scene name='86/865933/As_no_cartoon_labels_hbonds/1'>show hydrogen bonds</scene> within the active site, including those to the ligand, or measures polar contacts manually.		To show mastery, the learner will first focus on <scene name='86/865933/Unit_a/5'>subunit A of the complex</scene>, hiding subunit B for clarity. An <scene name='87/870565/Zoom_ligand_spacefill/1'>unobscured view of the ligand</scene> is obtained by rotating the macromolecule and zooming in. To display interactions, the learner will first replace the spacefilling representation of the ligand with a <scene name='86/865933/Zoom_ligand_stick/2'>stick representation</scene>. To view the interacting residues, the learner shows amino acid residues within 5Å of the active site <scene name='86/865933/Zoom_ligand_plus_as_stick/3'>as sticks and displays them with CPK coloring</scene>. For contrast, the learner colors the ligand magenta. In this view, water molecules within 5Å of the ligand are displayed as well. The view has gotten busy, so to focus in on the active site residues, the learner can <scene name='86/865933/As_no_cartoon/1'>hide the cartoon rendering of the protein</scene>, and then show the <scene name='86/865933/As_no_cartoon_with_labels/1'>active site residues with labels</scene>. The learner then executes a command to <scene name='86/865933/As_no_cartoon_labels_hbonds/1'>show hydrogen bonds</scene> within the active site, including those to the ligand, or measures polar contacts manually.

	</StructureSection>		</StructureSection>

Karsten Theis at 17:05, 10 February 2021

2021-02-10T17:05:14Z

← Older revision		Revision as of 17:05, 10 February 2021
Line 20:		Line 20:
	''Clicking on any of the green links in the following paragraph will show an example of how the learner's model may look at that stage of the process''		''Clicking on any of the green links in the following paragraph will show an example of how the learner's model may look at that stage of the process''

	To show mastery, the learner will first focus on <scene name='86/865933/Unit_a/5'>subunit A of the complex</scene>, hiding subunit B for clarity. An <scene name='86/865933/Zoom_ligand_spacefill/3'>unobscured view of the ligand</scene> is obtained by rotating the macromolecule and zooming in. To display interactions, the learner will first replace the spacefilling representation of the ligand with a <scene name='86/865933/Zoom_ligand_stick/2'>stick representation</scene>. To view the interacting residues, the learner shows amino acid residues within 5Å of the active site <scene name='86/865933/Zoom_ligand_plus_as_stick/3'>as sticks and displays them with CPK coloring</scene>. For contrast, the learner colors the ligand magenta. In this view, water molecules within 5Å of the ligand are displayed as well. The view has gotten busy, so to focus in on the active site residues, the learner can <scene name='86/865933/As_no_cartoon/1'>hide the cartoon rendering of the protein</scene>, and then show the <scene name='86/865933/As_no_cartoon_with_labels/1'>active site residues with labels</scene>. The learner then executes a command to <scene name='86/865933/As_no_cartoon_labels_hbonds/1'>show hydrogen bonds</scene> within the active site, including those to the ligand, or measures polar contacts manually.		To show mastery, the learner will first focus on <scene name='86/865933/Unit_a/5'>subunit A of the complex</scene>, hiding subunit B for clarity. An <scene name='86/865933/Zoom_ligand_spacefill/4'>unobscured view of the ligand</scene> is obtained by rotating the macromolecule and zooming in. To display interactions, the learner will first replace the spacefilling representation of the ligand with a <scene name='86/865933/Zoom_ligand_stick/2'>stick representation</scene>. To view the interacting residues, the learner shows amino acid residues within 5Å of the active site <scene name='86/865933/Zoom_ligand_plus_as_stick/3'>as sticks and displays them with CPK coloring</scene>. For contrast, the learner colors the ligand magenta. In this view, water molecules within 5Å of the ligand are displayed as well. The view has gotten busy, so to focus in on the active site residues, the learner can <scene name='86/865933/As_no_cartoon/1'>hide the cartoon rendering of the protein</scene>, and then show the <scene name='86/865933/As_no_cartoon_with_labels/1'>active site residues with labels</scene>. The learner then executes a command to <scene name='86/865933/As_no_cartoon_labels_hbonds/1'>show hydrogen bonds</scene> within the active site, including those to the ligand, or measures polar contacts manually.

	</StructureSection>		</StructureSection>

Kristen Procko at 21:02, 17 December 2020

2020-12-17T21:02:28Z

← Older revision		Revision as of 21:02, 17 December 2020
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	==An Example Assessment: Alternate Renderings (AR) Overarching Theme==		==An Example Assessment: Alternate Renderings (AR) Overarching Theme==
	<StructureSection load='2yvk' size='340' side='right' caption='Caption for this structure' scene=''>		<StructureSection load='2yvk' size='340' side='right' caption='Caption for this structure' scene=''>
	The broader goal of the BioMolViz project is to build a repository of assessments that instructors can use in their courses to evaluate visual literacy gains. These assessments are written in teams, peer reviewed, and will undergo validation by an expert panel. Using the Framework, these assessments are designed from the learning objectives. The twelve overarching themes of the BioMolviz Framework, and the associated learning goals and objectives, can be viewed on the [~~https~~://biomolviz.org/framework/ BioMolViz website].		The broader goal of the [http://proteopedia.org/wiki/index.php/The_BioMolViz_Project BioMolViz project] is to build a repository of assessments that instructors can use in their courses to evaluate visual literacy gains. These assessments are written in teams, peer reviewed, and will undergo validation by an expert panel. Using the Framework, these assessments are designed from the learning objectives. The twelve overarching themes of the BioMolviz Framework, and the associated learning goals and objectives, can be viewed on the [http://biomolviz.org/framework/ BioMolViz website].

	As an example, a repository contributor might identify the '''[[:Category:Alternate Renderings\|Alternate Renderings (AR)]]''' Overarching Theme as an area they wish to target with their assessment. One '''learning goal''' within the AR theme is:		As an example, a repository contributor might identify the '''[[:Category:Alternate Renderings\|Alternate Renderings (AR)]]''' Overarching Theme as an area they wish to target with their assessment. One '''learning goal''' within the AR theme is:

Kristen Procko: New page: ==An Example Assessment: Alternate Renderings (AR) Overarching Theme== The broader goal...

2020-12-17T20:58:56Z

New page: ==An Example Assessment: Alternate Renderings (AR) Overarching Theme== <StructureSection load='2yvk' size='340' side='right' caption='Caption for this structure' scene=''> The broader goal...

New page

==An Example Assessment: Alternate Renderings (AR) Overarching Theme==
<StructureSection load='2yvk' size='340' side='right' caption='Caption for this structure' scene=''>
The broader goal of the BioMolViz project is to build a repository of assessments that instructors can use in their courses to evaluate visual literacy gains. These assessments are written in teams, peer reviewed, and will undergo validation by an expert panel. Using the Framework, these assessments are designed from the learning objectives. The twelve overarching themes of the BioMolviz Framework, and the associated learning goals and objectives, can be viewed on the [https://biomolviz.org/framework/ BioMolViz website].

As an example, a repository contributor might identify the '''[[:Category:Alternate Renderings|Alternate Renderings (AR)]]''' Overarching Theme as an area they wish to target with their assessment. One '''learning goal''' within the AR theme is:

:'''AR1''': Students can create meaningful molecular images to convey features such as secondary structure, CPK coloring, active sites and molecular interactions.

A '''learning objective''' encompassed by this goal is:

:'''AR1.04:''' Students can infer information from rendering a structure in different ways.

An '''assessment''' that can be used test if this learning objective has been met can explore protein-ligand interactions. An example of how this assessment may be described to the learner is provided below.

:''Given the structure of 5-methylthioribose 1-phosphate(MTRu-1-P) isomerase bound to MTRu-1-P (PDB ID: 2yvk chain A), use Jmol (or another molecular visualization tool such as Chimera or PyMOL) to identify the amino acids in the protein that interact with the ligand.''

'''Example Assessment Solution'''

''Clicking on any of the green links in the following paragraph will show an example of how the learner's model may look at that stage of the process''

To show mastery, the learner will first focus on <scene name='86/865933/Unit_a/5'>subunit A of the complex</scene>, hiding subunit B for clarity. An <scene name='86/865933/Zoom_ligand_spacefill/3'>unobscured view of the ligand</scene> is obtained by rotating the macromolecule and zooming in. To display interactions, the learner will first replace the spacefilling representation of the ligand with a <scene name='86/865933/Zoom_ligand_stick/2'>stick representation</scene>. To view the interacting residues, the learner shows amino acid residues within 5Å of the active site <scene name='86/865933/Zoom_ligand_plus_as_stick/3'>as sticks and displays them with CPK coloring</scene>. For contrast, the learner colors the ligand magenta. In this view, water molecules within 5Å of the ligand are displayed as well. The view has gotten busy, so to focus in on the active site residues, the learner can <scene name='86/865933/As_no_cartoon/1'>hide the cartoon rendering of the protein</scene>, and then show the <scene name='86/865933/As_no_cartoon_with_labels/1'>active site residues with labels</scene>. The learner then executes a command to <scene name='86/865933/As_no_cartoon_labels_hbonds/1'>show hydrogen bonds</scene> within the active site, including those to the ligand, or measures polar contacts manually.

</StructureSection>
== References ==
<references/>
Bateman, Robert C., and Paul A. Craig. 2010. “Education Corner: A Proficiency Rubric for Biomacromolecular 3D Literacy.” PDB Newsletter 45: 5–7.

Dries, Daniel R., Diane M. Dean, Laura L. Listenberger, Walter R.P. Novak, Margaret A. Franzen, and Paul A. Craig. 2016. “An Expanded Framework for Biomolecular Visualization in the Classroom: Learning Goals and Competencies.” Biochemistry and Molecular Biology Education. https://doi.org/10.1002/bmb.20991.
<references/>

[[Category: BioMolViz]]
[[Category: Alternate Renderings]]