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In this tutorial, we will use lysozyme bound to a <scene name='79/797412/Carb/2'>carbohydrate</scene> as our example structure. In the <scene name='79/797412/Overall/1'>opening scene</scene>, the protein is shown in deepskyblue as a carbon alpha trace, and the carbohydrate is shown in all-bonds, colored using the [[CPK]] color scheme. Lysozyme was the [[Highest_impact_structures|first enzyme structure]] to be solved. | In this tutorial, we will use lysozyme bound to a <scene name='79/797412/Carb/2'>carbohydrate</scene> as our example structure. In the <scene name='79/797412/Overall/1'>opening scene</scene>, the protein is shown in deepskyblue as a carbon alpha trace, and the carbohydrate is shown in all-bonds, colored using the [[CPK]] color scheme. Lysozyme was the [[Highest_impact_structures|first enzyme structure]] to be solved. | ||
==Basic reading and viewing== | ==Basic reading and viewing== | ||
*Read the text: Read the text (tell your browser if you need a bigger font by clicking control-plus) and use the scroll bar on the right to navigate. Don't follow any [http://www.google.com hyperlinks] directly (because you will have to reload the proteopedia page if you do). If you want to check out a hyperlink, try right-clicking it to open the link in a new tab of your browser. | *Read the text: Read the text (tell your browser if you need a bigger font by clicking control-plus) and use the scroll bar on the right to navigate. Don't follow any [http://www.google.com hyperlinks] directly (because you will have to reload the proteopedia page if you do). If you want to check out a hyperlink, try right-clicking it to open the link in a new tab of your browser. | ||
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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? | ||
<StructureSection load='' size='500' side='right' caption='Caption for this structure' scene='79/797412/Overall/1'> | |||
==Using the mouse== | ==Using the mouse== | ||
*Identifying atoms: Make sure the molecule is not spinning on its own (you can turn that off in the 3D browser by clickling 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. Something like "[ALA]23:A.CA #252" should have appeared, which would tell you this atom is part of an alanine residue with residue number 23 of chain (or subunit) A. The atom is an alpha carbon (CA) and is atom number 252 in the coordinate file. | *Identifying atoms: Make sure the molecule is not spinning on its own (you can turn that off in the 3D browser by clickling 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. Something like "[ALA]23:A.CA #252" should have appeared, which would tell you this atom is part of an alanine residue with residue number 23 of chain (or subunit) A. The atom is an alpha carbon (CA) and is atom number 252 in the coordinate file. | ||
