User:Eleanor Crabb/Sandbox 1 - Revision history

Eleanor Crabb at 15:41, 20 October 2009

Eleanor Crabb — Tue, 20 Oct 2009 15:41:09 GMT

←Older revision		Revision as of 15:41, 20 October 2009
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-	<applet load='1z3a' size='300' frame='true' align='right' caption='~~Insert caption here~~' />This page is designed to be an introduction to protein structure and the 3D visualisation package Jmol used here in Proteopedia and also on the RCSB Protein Data Bank to visualise proteins.	+
-	The interactive image on the right shows the '''asymmetric unit''' of ta zinc ~~containg~~ enzyme with the pdb code 1z3a. (The asymmetric unit is the smallest part of the crystal structure that can be used to generate the unit cell of a crystal and hence the entire crystal structure of a protein - see the asymmetric tutorial at the RCSB Protein Data Bank [http://www.rcsb.org/pdb/static.do?p=education_discussion/Looking-at-Structures/biounit_tutorial.html#Anchor-Asym]for more information.)	+	== Visualising Protein Structure ==
		+	<applet load='1z3a' size='300' frame='true' align='right' caption='1z3a' />This page is designed to be an introduction to protein structure and the 3D visualisation package, '''Jmol''', used here in Proteopedia and also on the RCSB Protein Data Bank website to visualise proteins.
		+	The interactive image on the right shows the '''asymmetric unit''' of a zinc-containing enzyme with the pdb code '''1z3a'''. (The asymmetric unit is the smallest part of the crystal structure that can be used to generate the unit cell of a crystal and hence the entire crystal structure of a protein - see the asymmetric tutorial at the RCSB Protein Data Bank [http://www.rcsb.org/pdb/static.do?p=education_discussion/Looking-at-Structures/biounit_tutorial.html#Anchor-Asym] for more information.)

-	You can rotate the molecule using your mouse and zoom in and out by holding down the shift key while you move the mouse. You can also spin the molecule use the Toggle spin button below the molecule.	+	You can rotate the molecule using your mouse and zoom in and out by holding down the shift key while you move the mouse. You can also spin the molecule use the Toggle spin button below the molecule. (The popup button will open a resizable Jmol representation of the molecule in another window.)

-	You will note that there are two chains in this protein, shown in green and blue. For simplicity let us concentrate on just a <scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain/1'>single chain</scene>, chain A. To see just chain A, click on the link in green. If you hover the mouse over a particular part of the structure, for example, the central zinc atom, you will see a yellow box with a label giving the atom identity. In this example, ~~if you hover your cursor over the grey atom~~ you will see the label [[Image:elementbox.JPG]]. Hovering the cursor over the ~~grey~~ backbone of the protein will show the constituent residues in the chain.	+	You will note that there are two chains in this protein, shown in green and blue. For simplicity let us concentrate on just a <scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain/1'>single chain</scene>, chain A. To see just chain A, click on the link in green. If you hover the mouse over a particular part of the structure, for example, the central zinc atom, you will see a yellow box with a label giving the atom identity. In this example, you will see the label [[Image:elementbox.JPG]]. Hovering the cursor over the backbone of the protein will show the constituent residues in the chain.

	This is a cartoon representation of the protein, showing a schematic representation of the back bone of the protein. You may be more familiar with the following molecular representations (note in all cases that the H atoms in the molecule are not shown):		This is a cartoon representation of the protein, showing a schematic representation of the back bone of the protein. You may be more familiar with the following molecular representations (note in all cases that the H atoms in the molecule are not shown):

-	*<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_a_sfllcolour/2'>space- filled</scene> - this gives an indication of the size and shape of the protein	+	*<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_a_sfllcolour/2'>space-filled</scene> - this gives an indication of the size and shape of the protein
-	*<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_a_ballcolour/1'>ball and stick</scene> - this view allows you to see ~~more clearly~~ the atoms in the protein.	+	*<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_a_ballcolour/1'>ball and stick</scene> - this view allows you to see the atoms in the protein.

	Now, let us simplify things further by looking at just a		Now, let us simplify things further by looking at just a
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	<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_helix/1'>cartoon</scene> alone.		<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_helix/1'>cartoon</scene> alone.

-	~~Returning now to <scene name='User:~~Eleanor_Crabb/~~Sandbox_1/1z3a_single_chain/1'>Chain A</scene>. This can be coloured according to:~~	+	[[Eleanor_Crabb/The_four_tiers_of_protein_structure\|Next page - The four tiers of protein structure]]
-	*the arrangement of ~~the <scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain_res/1'>residues</scene> Hover your cursor over the molecule to identify some of the different residues in the chain.~~	+
-		+
-	*<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain_nc/1'>NC</scene>	+
-	*<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain_2nd/1'>Secondary structure~~</scene>~~	+
-		+
-	~~Finally, focussing now on the zinc atom <scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_a_active_site2/1'>residues within 30 nm</scene>~~	+

Eleanor Crabb at 22:07, 8 October 2009

Eleanor Crabb — Thu, 08 Oct 2009 22:07:19 GMT

←Older revision		Revision as of 22:07, 8 October 2009
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	The interactive image on the right shows the '''asymmetric unit''' of ta zinc containg enzyme with the pdb code 1z3a. (The asymmetric unit is the smallest part of the crystal structure that can be used to generate the unit cell of a crystal and hence the entire crystal structure of a protein - see the asymmetric tutorial at the RCSB Protein Data Bank [http://www.rcsb.org/pdb/static.do?p=education_discussion/Looking-at-Structures/biounit_tutorial.html#Anchor-Asym]for more information.)		The interactive image on the right shows the '''asymmetric unit''' of ta zinc containg enzyme with the pdb code 1z3a. (The asymmetric unit is the smallest part of the crystal structure that can be used to generate the unit cell of a crystal and hence the entire crystal structure of a protein - see the asymmetric tutorial at the RCSB Protein Data Bank [http://www.rcsb.org/pdb/static.do?p=education_discussion/Looking-at-Structures/biounit_tutorial.html#Anchor-Asym]for more information.)

-	You can rotate the molecule using your mouse and zoom in and out by holding down the shift key while you move the mouse.	+	You can rotate the molecule using your mouse and zoom in and out by holding down the shift key while you move the mouse. You can also spin the molecule use the Toggle spin button below the molecule.

-	You will note that there are two chains in this protein, shown in green and blue. For simplicity let us concentrate on just a <scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain/1'>single chain</scene>, chain A. To see ~~this~~ click on the link in green. If you hover the mouse over a particular part of the structure, for example, the central zinc atom, you will see a yellow box with a label giving the atom identity. In this example, you will see the label [[Image:elementbox.JPG]]	+	You will note that there are two chains in this protein, shown in green and blue. For simplicity let us concentrate on just a <scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain/1'>single chain</scene>, chain A. To see just chain A, click on the link in green. If you hover the mouse over a particular part of the structure, for example, the central zinc atom, you will see a yellow box with a label giving the atom identity. In this example, if you hover your cursor over the grey atom you will see the label [[Image:elementbox.JPG]]. Hovering the cursor over the grey backbone of the protein will show the constituent residues in the chain.

	This is a cartoon representation of the protein, showing a schematic representation of the back bone of the protein. You may be more familiar with the following molecular representations (note in all cases that the H atoms in the molecule are not shown):		This is a cartoon representation of the protein, showing a schematic representation of the back bone of the protein. You may be more familiar with the following molecular representations (note in all cases that the H atoms in the molecule are not shown):

	*<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_a_sfllcolour/2'>space- filled</scene> - this gives an indication of the size and shape of the protein		*<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_a_sfllcolour/2'>space- filled</scene> - this gives an indication of the size and shape of the protein
-	*<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_a_ballcolour/1'>ball and stick</scene>	+	*<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_a_ballcolour/1'>ball and stick</scene> - this view allows you to see more clearly the atoms in the protein.

-	~~Let~~ us simplify things further by looking at just a	+	Now, let us simplify things further by looking at just a
	<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_helix_ball/1'>small portion </scene> of the chain. If you rotate the model you can clearly see the backbone linking the different residues. We now draw a line through the backbone of the chain illustrated as <scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_helix_ballcartoon/1'>the cartoon with the residues</scene> or the		<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_helix_ball/1'>small portion </scene> of the chain. If you rotate the model you can clearly see the backbone linking the different residues. We now draw a line through the backbone of the chain illustrated as <scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_helix_ballcartoon/1'>the cartoon with the residues</scene> or the
-	<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_helix/1'>cartoon</scene> alone.	+	<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_helix/1'>cartoon</scene> alone.

	Returning now to <scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain/1'>Chain A</scene>. This can be coloured according to:		Returning now to <scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain/1'>Chain A</scene>. This can be coloured according to:
-	*the arrangement of the <scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain_res/1'>residues</scene>	+	*the arrangement of the <scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain_res/1'>residues</scene> Hover your cursor over the molecule to identify some of the different residues in the chain.

	*<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain_nc/1'>NC</scene>		*<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain_nc/1'>NC</scene>

Eleanor Crabb at 21:59, 8 October 2009

Eleanor Crabb — Thu, 08 Oct 2009 21:59:29 GMT

←Older revision		Revision as of 21:59, 8 October 2009
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	You can rotate the molecule using your mouse and zoom in and out by holding down the shift key while you move the mouse.		You can rotate the molecule using your mouse and zoom in and out by holding down the shift key while you move the mouse.

-	You will note that there are two chains in this protein, shown in green and blue. For simplicity let us concentrate on just a <scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain/1'>single chain</scene>, chain A. To see this click on the link in green. If you hover the mouse over a particular part of the structure, for example, the central zinc atom, you will see a yellow box with a label giving the atom identity. In this example, you will see the label [[Image:elementbox.~~jpg~~]]	+	You will note that there are two chains in this protein, shown in green and blue. For simplicity let us concentrate on just a <scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain/1'>single chain</scene>, chain A. To see this click on the link in green. If you hover the mouse over a particular part of the structure, for example, the central zinc atom, you will see a yellow box with a label giving the atom identity. In this example, you will see the label [[Image:elementbox.JPG]]

	This is a cartoon representation of the protein, showing a schematic representation of the back bone of the protein. You may be more familiar with the following molecular representations (note in all cases that the H atoms in the molecule are not shown):		This is a cartoon representation of the protein, showing a schematic representation of the back bone of the protein. You may be more familiar with the following molecular representations (note in all cases that the H atoms in the molecule are not shown):

Eleanor Crabb at 21:58, 8 October 2009

Eleanor Crabb — Thu, 08 Oct 2009 21:58:18 GMT

←Older revision		Revision as of 21:58, 8 October 2009
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	You can rotate the molecule using your mouse and zoom in and out by holding down the shift key while you move the mouse.		You can rotate the molecule using your mouse and zoom in and out by holding down the shift key while you move the mouse.

-	You will note that there are two chains in this protein, shown in green and blue. For simplicity let us concentrate on just a <scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain/1'>single chain</scene>, chain A. To see this click on the link in green. If you hover the mouse over a particular part of the structure, for example, the central zinc atom, you will see a yellow box with a label giving the atom identity. In this example, you will see [[Image:~~Example~~.jpg]]	+	You will note that there are two chains in this protein, shown in green and blue. For simplicity let us concentrate on just a <scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain/1'>single chain</scene>, chain A. To see this click on the link in green. If you hover the mouse over a particular part of the structure, for example, the central zinc atom, you will see a yellow box with a label giving the atom identity. In this example, you will see the label [[Image:elementbox.jpg]]

	This is a cartoon representation of the protein, showing a schematic representation of the back bone of the protein. You may be more familiar with the following molecular representations (note in all cases that the H atoms in the molecule are not shown):		This is a cartoon representation of the protein, showing a schematic representation of the back bone of the protein. You may be more familiar with the following molecular representations (note in all cases that the H atoms in the molecule are not shown):

Eleanor Crabb at 21:52, 8 October 2009

Eleanor Crabb — Thu, 08 Oct 2009 21:52:24 GMT

←Older revision		Revision as of 21:52, 8 October 2009
Line 4:		Line 4:
	You can rotate the molecule using your mouse and zoom in and out by holding down the shift key while you move the mouse.		You can rotate the molecule using your mouse and zoom in and out by holding down the shift key while you move the mouse.

-	You will note that there are two chains in this protein, shown in green and blue. For simplicity let us concentrate on just a <scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain/1'>single chain</scene>, chain A. To see this click on the link in green. If you hover the mouse over a particular part of the structure, for example, the central zinc atom, you will see a yellow box with a label giving the atom identity. In this example, you will see ~~ZN 301, Chain A Element Zn~~	+	You will note that there are two chains in this protein, shown in green and blue. For simplicity let us concentrate on just a <scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain/1'>single chain</scene>, chain A. To see this click on the link in green. If you hover the mouse over a particular part of the structure, for example, the central zinc atom, you will see a yellow box with a label giving the atom identity. In this example, you will see [[Image:Example.jpg]]

	This is a cartoon representation of the protein, showing a schematic representation of the back bone of the protein. You may be more familiar with the following molecular representations (note in all cases that the H atoms in the molecule are not shown):		This is a cartoon representation of the protein, showing a schematic representation of the back bone of the protein. You may be more familiar with the following molecular representations (note in all cases that the H atoms in the molecule are not shown):

Eleanor Crabb at 21:49, 8 October 2009

Eleanor Crabb — Thu, 08 Oct 2009 21:49:18 GMT

←Older revision		Revision as of 21:49, 8 October 2009
Line 4:		Line 4:
	You can rotate the molecule using your mouse and zoom in and out by holding down the shift key while you move the mouse.		You can rotate the molecule using your mouse and zoom in and out by holding down the shift key while you move the mouse.

-	You will note that there are two chains in this protein, shown in green and blue. For simplicity let us concentrate on just a <scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain/1'>single chain</scene>, chain A. To see this click on the link in green. If you hover the mouse over a particular part of the structure, for example, the central zinc atom, you will see a yellow box with a label giving the atom identity. In this example,	+	You will note that there are two chains in this protein, shown in green and blue. For simplicity let us concentrate on just a <scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain/1'>single chain</scene>, chain A. To see this click on the link in green. If you hover the mouse over a particular part of the structure, for example, the central zinc atom, you will see a yellow box with a label giving the atom identity. In this example, you will see ZN 301, Chain A Element Zn

	This is a cartoon representation of the protein, showing a schematic representation of the back bone of the protein. You may be more familiar with the following molecular representations (note in all cases that the H atoms in the molecule are not shown):		This is a cartoon representation of the protein, showing a schematic representation of the back bone of the protein. You may be more familiar with the following molecular representations (note in all cases that the H atoms in the molecule are not shown):

Eleanor Crabb at 21:46, 8 October 2009

Eleanor Crabb — Thu, 08 Oct 2009 21:46:33 GMT

←Older revision		Revision as of 21:46, 8 October 2009
Line 1:		Line 1:
-	<applet load='1z3a' size='300' frame='true' align='right' caption='Insert caption here' />This page is designed to be an introduction to protein structure and the 3D visualisation package ~~JMOL~~ used here in Proteopedia and also on the Protein Data Bank to visualise proteins.	+	<applet load='1z3a' size='300' frame='true' align='right' caption='Insert caption here' />This page is designed to be an introduction to protein structure and the 3D visualisation package Jmol used here in Proteopedia and also on the RCSB Protein Data Bank to visualise proteins.
-	The interactive image on the right shows the ~~protein~~ with the pdb code 1z3a. You can rotate the molecule using your mouse and zoom by holding down the shift key while you move the mouse~~. Mention hover and zn~~.	+	The interactive image on the right shows the '''asymmetric unit''' of ta zinc containg enzyme with the pdb code 1z3a. (The asymmetric unit is the smallest part of the crystal structure that can be used to generate the unit cell of a crystal and hence the entire crystal structure of a protein - see the asymmetric tutorial at the RCSB Protein Data Bank [http://www.rcsb.org/pdb/static.do?p=education_discussion/Looking-at-Structures/biounit_tutorial.html#Anchor-Asym]for more information.)
		+
		+	You can rotate the molecule using your mouse and zoom in and out by holding down the shift key while you move the mouse.

-	You will note that there are two chains in this protein,shown in green and blue. For simplicity let us concentrate on just a <scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain/1'>single chain</scene>, chain A. To see this click on the link in green.	+	You will note that there are two chains in this protein, shown in green and blue. For simplicity let us concentrate on just a <scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain/1'>single chain</scene>, chain A. To see this click on the link in green. If you hover the mouse over a particular part of the structure, for example, the central zinc atom, you will see a yellow box with a label giving the atom identity. In this example,

-	This is a cartoon representation of the protein, showing a schematic representation of the back bone of the protein. You may be more familiar with the following molecular representations (note that the H atoms are not shown):	+	This is a cartoon representation of the protein, showing a schematic representation of the back bone of the protein. You may be more familiar with the following molecular representations (note in all cases that the H atoms in the molecule are not shown):

	*<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_a_sfllcolour/2'>space- filled</scene> - this gives an indication of the size and shape of the protein		*<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_a_sfllcolour/2'>space- filled</scene> - this gives an indication of the size and shape of the protein

Eleanor Crabb at 11:27, 29 September 2009

Eleanor Crabb — Tue, 29 Sep 2009 11:27:14 GMT

←Older revision		Revision as of 11:27, 29 September 2009
Line 1:		Line 1:
	<applet load='1z3a' size='300' frame='true' align='right' caption='Insert caption here' />This page is designed to be an introduction to protein structure and the 3D visualisation package JMOL used here in Proteopedia and also on the Protein Data Bank to visualise proteins.		<applet load='1z3a' size='300' frame='true' align='right' caption='Insert caption here' />This page is designed to be an introduction to protein structure and the 3D visualisation package JMOL used here in Proteopedia and also on the Protein Data Bank to visualise proteins.
-	The interactive image on the right shows the protein with the pdb code 1z3a. You can rotate the molecule using your mouse and zoom by holding down the shift key while you move the mouse.	+	The interactive image on the right shows the protein with the pdb code 1z3a. You can rotate the molecule using your mouse and zoom by holding down the shift key while you move the mouse. Mention hover and zn.

	You will note that there are two chains in this protein,shown in green and blue. For simplicity let us concentrate on just a <scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain/1'>single chain</scene>, chain A. To see this click on the link in green.		You will note that there are two chains in this protein,shown in green and blue. For simplicity let us concentrate on just a <scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain/1'>single chain</scene>, chain A. To see this click on the link in green.

Eleanor Crabb at 22:02, 18 September 2009

Eleanor Crabb — Fri, 18 Sep 2009 22:02:39 GMT

←Older revision		Revision as of 22:02, 18 September 2009
Line 6:		Line 6:
	This is a cartoon representation of the protein, showing a schematic representation of the back bone of the protein. You may be more familiar with the following molecular representations (note that the H atoms are not shown):		This is a cartoon representation of the protein, showing a schematic representation of the back bone of the protein. You may be more familiar with the following molecular representations (note that the H atoms are not shown):

-	*<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_a_sfllcolour/1'>space- filled</scene> - this gives an indication of the size and shape of the protein	+	*<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_a_sfllcolour/2'>space- filled</scene> - this gives an indication of the size and shape of the protein
	*<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_a_ballcolour/1'>ball and stick</scene>		*<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_a_ballcolour/1'>ball and stick</scene>

Line 14:		Line 14:

	Returning now to <scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain/1'>Chain A</scene>. This can be coloured according to:		Returning now to <scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain/1'>Chain A</scene>. This can be coloured according to:
-	*the arrangement of the<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain_res/1'>residues</scene>	+	*the arrangement of the <scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain_res/1'>residues</scene>

	*<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain_nc/1'>NC</scene>		*<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain_nc/1'>NC</scene>
	*<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain_2nd/1'>Secondary structure</scene>		*<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain_2nd/1'>Secondary structure</scene>

-	Finally, focussing now on the zinc atom <scene name='User:Eleanor_Crabb/Sandbox_1/~~1z3a_a_active_site~~/1'>residues within 30 nm</scene>	+	Finally, focussing now on the zinc atom <scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_a_active_site2/1'>residues within 30 nm</scene>

Eleanor Crabb at 21:58, 18 September 2009

Eleanor Crabb — Fri, 18 Sep 2009 21:58:27 GMT

←Older revision		Revision as of 21:58, 18 September 2009
Line 10:		Line 10:

	Let us simplify things further by looking at just a		Let us simplify things further by looking at just a
-	<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_helix_ball/1'>small portion </scene> of the chain. If we now draw a line through the backbone of the chain illustrated as <scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_helix_ballcartoon/1'>the cartoon with the residues</scene> or the	+	<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_helix_ball/1'>small portion </scene> of the chain. If you rotate the model you can clearly see the backbone linking the different residues. We now draw a line through the backbone of the chain illustrated as <scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_helix_ballcartoon/1'>the cartoon with the residues</scene> or the
	<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_helix/1'>cartoon</scene> alone.		<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_helix/1'>cartoon</scene> alone.

	Returning now to <scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain/1'>Chain A</scene>. This can be coloured according to:		Returning now to <scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain/1'>Chain A</scene>. This can be coloured according to:
-	*the arrangement of the ~~residues is the primary structure coloured according to~~ <scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain_res/1'>~~residue~~</scene>.	+	*the arrangement of the<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain_res/1'>residues</scene>

	*<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain_nc/1'>NC</scene>		*<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain_nc/1'>NC</scene>
	*<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain_2nd/1'>Secondary structure</scene>		*<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_single_chain_2nd/1'>Secondary structure</scene>

-	<scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_a_active_site/1'>residues within 30 nm</scene>	+	Finally, focussing now on the zinc atom <scene name='User:Eleanor_Crabb/Sandbox_1/1z3a_a_active_site/1'>residues within 30 nm</scene>