Help:Viewing pages - Revision history

Karsten Theis: Help:Viewing moved to Help:Viewing pages

Karsten Theis — Tue, 16 Feb 2021 16:46:16 GMT

Help:Viewing moved to Help:Viewing pages

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Revision as of 16:46, 16 February 2021

Karsten Theis: Viewing guide moved to Help:Viewing: Easier to find help page

Karsten Theis — Tue, 16 Feb 2021 16:44:45 GMT

Viewing guide moved to Help:Viewing: Easier to find help page

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Revision as of 16:44, 16 February 2021

Angel Herraez: link to the Spanish traslation

Angel Herraez — Wed, 14 Oct 2020 18:50:15 GMT

link to the Spanish traslation

←Older revision		Revision as of 18:50, 14 October 2020
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		+	[[es:Viewing guide (Spanish)]]
	This is a brief tutorial on how to read a Proteopedia article and view the integrated 3D figures. A single page [http://proteopedia.org/wiki/index.php/Image:ProteopediaViewingGuide.pdf cheat sheet] is available. We will use lysozyme bound to a <scene name='79/797412/Carb/3'>carbohydrate</scene> as our example structure. In the <scene name='79/797412/Overall/3'>opening scene</scene>, the protein is shown in blue ("deep sky blue", to be exact) as a carbon alpha trace, and the carbohydrate is shown in all-bonds, colored using the [[CPK\|CPK color scheme]]. Lysozyme was the [[Highest_impact_structures\|first enzyme structure]] to be solved.		This is a brief tutorial on how to read a Proteopedia article and view the integrated 3D figures. A single page [http://proteopedia.org/wiki/index.php/Image:ProteopediaViewingGuide.pdf cheat sheet] is available. We will use lysozyme bound to a <scene name='79/797412/Carb/3'>carbohydrate</scene> as our example structure. In the <scene name='79/797412/Overall/3'>opening scene</scene>, the protein is shown in blue ("deep sky blue", to be exact) as a carbon alpha trace, and the carbohydrate is shown in all-bonds, colored using the [[CPK\|CPK color scheme]]. Lysozyme was the [[Highest_impact_structures\|first enzyme structure]] to be solved.

Karsten Theis at 00:06, 2 October 2020

Karsten Theis — Fri, 02 Oct 2020 00:06:50 GMT

←Older revision		Revision as of 00:06, 2 October 2020
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	*'''Use the mouse''' to rotate the 3D figure: To really appreciate the three-dimensional nature of proteins and other molecules, you should drag the molecule to change the view. Imagine that when you drag, you are holding on to the atoms in the foreground, and dragging them while the center of rotation stays put. Try it! After rotating the molecules, can you see any features that were hidden before? Does it become easier to visualize the three-dimensional shape as you move the molecule?		*'''Use the mouse''' to rotate the 3D figure: To really appreciate the three-dimensional nature of proteins and other molecules, you should drag the molecule to change the view. Imagine that when you drag, you are holding on to the atoms in the foreground, and dragging them while the center of rotation stays put. Try it! After rotating the molecules, can you see any features that were hidden before? Does it become easier to visualize the three-dimensional shape as you move the molecule?

-	==Using the mouse==	+	==Using the mouse cont.==
	*'''Identify atoms''': Make sure the molecule is not spinning on its own (you can turn that off in the 3D browser by clicking the "± spin" text on the bottom). Then, hover (i.e. point with the mouse pointer without moving or clicking) over an atom, and a small pop-up text will appear. Try it! Here is an example text: "[ALA]23:A.CA #252" illustrating the format. It shows that the atom hovered over is part of alanine (ALA) residue number 23 of chain A (or subunit A). The atom is an alpha carbon (CA) and has the serial number 252 in the coordinate file.		*'''Identify atoms''': Make sure the molecule is not spinning on its own (you can turn that off in the 3D browser by clicking the "± spin" text on the bottom). Then, hover (i.e. point with the mouse pointer without moving or clicking) over an atom, and a small pop-up text will appear. Try it! Here is an example text: "[ALA]23:A.CA #252" illustrating the format. It shows that the atom hovered over is part of alanine (ALA) residue number 23 of chain A (or subunit A). The atom is an alpha carbon (CA) and has the serial number 252 in the coordinate file.
	*'''Press shift''': When you press shift while dragging the molecule, the mouse pointer will look differently, and behave differently. Now, dragging up and down will zoom in or out, and dragging left and right will rotate the molecule around the z-axis. Try it! If your screen is touch-sensitive, you can also zoom with the usual two-finger pinch gestures. To move (translate) the molecule, press shift, double-click and drag. If your screen is touch-sensitve, you can also drag with two fingers. Try it! After you moved the molecule, it will still rotate around the old center of rotation (below we'll discuss how you can use the menu to change the center of rotation).		*'''Press shift''': When you press shift while dragging the molecule, the mouse pointer will look differently, and behave differently. Now, dragging up and down will zoom in or out, and dragging left and right will rotate the molecule around the z-axis. Try it! If your screen is touch-sensitive, you can also zoom with the usual two-finger pinch gestures. To move (translate) the molecule, press shift, double-click and drag. If your screen is touch-sensitve, you can also drag with two fingers. Try it! After you moved the molecule, it will still rotate around the old center of rotation (below we'll discuss how you can use the menu to change the center of rotation).

Karsten Theis at 17:03, 30 September 2020

Karsten Theis — Wed, 30 Sep 2020 17:03:45 GMT

←Older revision		Revision as of 17:03, 30 September 2020
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-	This is a brief tutorial on how to read a Proteopedia article and view the integrated 3D figures. A single page [[Image:ProteopediaViewingGuide.pdf\| cheat sheet]] is available. We will use lysozyme bound to a <scene name='79/797412/Carb/3'>carbohydrate</scene> as our example structure. In the <scene name='79/797412/Overall/3'>opening scene</scene>, the protein is shown in blue ("deep sky blue", to be exact) as a carbon alpha trace, and the carbohydrate is shown in all-bonds, colored using the [[CPK\|CPK color scheme]]. Lysozyme was the [[Highest_impact_structures\|first enzyme structure]] to be solved.	+	This is a brief tutorial on how to read a Proteopedia article and view the integrated 3D figures. A single page [http://proteopedia.org/wiki/index.php/Image:ProteopediaViewingGuide.pdf cheat sheet] is available. We will use lysozyme bound to a <scene name='79/797412/Carb/3'>carbohydrate</scene> as our example structure. In the <scene name='79/797412/Overall/3'>opening scene</scene>, the protein is shown in blue ("deep sky blue", to be exact) as a carbon alpha trace, and the carbohydrate is shown in all-bonds, colored using the [[CPK\|CPK color scheme]]. Lysozyme was the [[Highest_impact_structures\|first enzyme structure]] to be solved.

	<StructureSection load='' size='500' side='right' caption='Structure of the enzyme lysozyme (blue) in complex with carbohydrate (gray, red and blue)' scene='79/797412/Overall/3'>		<StructureSection load='' size='500' side='right' caption='Structure of the enzyme lysozyme (blue) in complex with carbohydrate (gray, red and blue)' scene='79/797412/Overall/3'>

Karsten Theis at 14:26, 13 September 2019

Karsten Theis — Fri, 13 Sep 2019 14:26:57 GMT

←Older revision		Revision as of 14:26, 13 September 2019
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-	This is a brief tutorial on how to read a Proteopedia article and view the integrated 3D figures. A single page [Image:ProteopediaViewingGuide.pdf\|cheat sheet] is available. We will use lysozyme bound to a <scene name='79/797412/Carb/3'>carbohydrate</scene> as our example structure. In the <scene name='79/797412/Overall/3'>opening scene</scene>, the protein is shown in blue ("deep sky blue", to be exact) as a carbon alpha trace, and the carbohydrate is shown in all-bonds, colored using the [[CPK\|CPK color scheme]]. Lysozyme was the [[Highest_impact_structures\|first enzyme structure]] to be solved.	+	This is a brief tutorial on how to read a Proteopedia article and view the integrated 3D figures. A single page [[Image:ProteopediaViewingGuide.pdf\| cheat sheet]] is available. We will use lysozyme bound to a <scene name='79/797412/Carb/3'>carbohydrate</scene> as our example structure. In the <scene name='79/797412/Overall/3'>opening scene</scene>, the protein is shown in blue ("deep sky blue", to be exact) as a carbon alpha trace, and the carbohydrate is shown in all-bonds, colored using the [[CPK\|CPK color scheme]]. Lysozyme was the [[Highest_impact_structures\|first enzyme structure]] to be solved.

	<StructureSection load='' size='500' side='right' caption='Structure of the enzyme lysozyme (blue) in complex with carbohydrate (gray, red and blue)' scene='79/797412/Overall/3'>		<StructureSection load='' size='500' side='right' caption='Structure of the enzyme lysozyme (blue) in complex with carbohydrate (gray, red and blue)' scene='79/797412/Overall/3'>

Karsten Theis at 14:23, 13 September 2019

Karsten Theis — Fri, 13 Sep 2019 14:23:30 GMT

←Older revision		Revision as of 14:23, 13 September 2019
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-	This is a brief tutorial on how to read a Proteopedia article and view the integrated 3D figures. A single page [[Image:ProteopediaViewingGuide.pdf\|cheat sheet]] is available. We will use lysozyme bound to a <scene name='79/797412/Carb/3'>carbohydrate</scene> as our example structure. In the <scene name='79/797412/Overall/3'>opening scene</scene>, the protein is shown in blue ("deep sky blue", to be exact) as a carbon alpha trace, and the carbohydrate is shown in all-bonds, colored using the [[CPK\|CPK color scheme]]. Lysozyme was the [[Highest_impact_structures\|first enzyme structure]] to be solved.	+	This is a brief tutorial on how to read a Proteopedia article and view the integrated 3D figures. A single page [Image:ProteopediaViewingGuide.pdf\|cheat sheet] is available. We will use lysozyme bound to a <scene name='79/797412/Carb/3'>carbohydrate</scene> as our example structure. In the <scene name='79/797412/Overall/3'>opening scene</scene>, the protein is shown in blue ("deep sky blue", to be exact) as a carbon alpha trace, and the carbohydrate is shown in all-bonds, colored using the [[CPK\|CPK color scheme]]. Lysozyme was the [[Highest_impact_structures\|first enzyme structure]] to be solved.

	<StructureSection load='' size='500' side='right' caption='Structure of the enzyme lysozyme (blue) in complex with carbohydrate (gray, red and blue)' scene='79/797412/Overall/3'>		<StructureSection load='' size='500' side='right' caption='Structure of the enzyme lysozyme (blue) in complex with carbohydrate (gray, red and blue)' scene='79/797412/Overall/3'>

Karsten Theis at 14:22, 13 September 2019

Karsten Theis — Fri, 13 Sep 2019 14:22:47 GMT

←Older revision		Revision as of 14:22, 13 September 2019
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-	This is a brief tutorial on how to read a Proteopedia article and view the integrated 3D figures. We will use lysozyme bound to a <scene name='79/797412/Carb/3'>carbohydrate</scene> as our example structure. In the <scene name='79/797412/Overall/3'>opening scene</scene>, the protein is shown in blue ("deep sky blue", to be exact) as a carbon alpha trace, and the carbohydrate is shown in all-bonds, colored using the [[CPK\|CPK color scheme]]. Lysozyme was the [[Highest_impact_structures\|first enzyme structure]] to be solved.	+	This is a brief tutorial on how to read a Proteopedia article and view the integrated 3D figures. A single page [[Image:ProteopediaViewingGuide.pdf\|cheat sheet]] is available. We will use lysozyme bound to a <scene name='79/797412/Carb/3'>carbohydrate</scene> as our example structure. In the <scene name='79/797412/Overall/3'>opening scene</scene>, the protein is shown in blue ("deep sky blue", to be exact) as a carbon alpha trace, and the carbohydrate is shown in all-bonds, colored using the [[CPK\|CPK color scheme]]. Lysozyme was the [[Highest_impact_structures\|first enzyme structure]] to be solved.

	<StructureSection load='' size='500' side='right' caption='Structure of the enzyme lysozyme (blue) in complex with carbohydrate (gray, red and blue)' scene='79/797412/Overall/3'>		<StructureSection load='' size='500' side='right' caption='Structure of the enzyme lysozyme (blue) in complex with carbohydrate (gray, red and blue)' scene='79/797412/Overall/3'>

Karsten Theis: User:Karsten Theis/viewing guide moved to Viewing guide: Make this tutorial accessible to everyone.

Karsten Theis — Thu, 16 May 2019 19:50:43 GMT

User:Karsten Theis/viewing guide moved to Viewing guide: Make this tutorial accessible to everyone.

←Older revision

Revision as of 19:50, 16 May 2019

Karsten Theis at 19:47, 16 May 2019

Karsten Theis — Thu, 16 May 2019 19:47:16 GMT

←Older revision		Revision as of 19:47, 16 May 2019
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	</StructureSection>		</StructureSection>
-
-	<scene name='79/797412/Overall/4'>test with caption</scene>
-	<scene name='79/797412/Overall/5'>test without caption</scene>

	Now you are ready to explore the fascinating world of proteins presented in Proteopedia!		Now you are ready to explore the fascinating world of proteins presented in Proteopedia!