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==Basic reading and viewing== | ==Basic reading and viewing== | ||
*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 (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. | ||
*Click on <scene name='79/797412/Carb/ | *Click on <scene name='79/797412/Carb/5'>the green links</scene>: While reading, as you encounter <scene name='79/797412/Overall/2'>text in green</scene>, click on it to get a new figure the the 3D window integrated into the text. Sometimes the 3D window is not visible on the screen, and you have to scroll up or down to find it. | ||
*Look at the 3D figures: The text should explain what you see. Is it an overall view or a zoomed-in detailed view? Do you know what the colors mean? Are there any labels? You can learn more about the depicted structure by using techniques explained in the following sections. If the figure is too small, either make it bigger using the magnifier glass at the bottom of the 3D window (this will squeeze the text, though) or open a new window using the popup control at the bottom of the 3D window (you will have to update this after clicking on green links, though). | *Look at the 3D figures: The text should explain what you see. Is it an overall view or a zoomed-in detailed view? Do you know what the colors mean? Are there any labels? You can learn more about the depicted structure by using techniques explained in the following sections. If the figure is too small, either make it bigger using the magnifier glass at the bottom of the 3D window (this will squeeze the text, though) or open a new window using the popup control at the bottom of the 3D window (you will have to update this after clicking on green links, though). | ||
*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? | ||
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*Selecting multiple parts of the molecule: When using the menu to select, each new selection command cancels the old one. Using the console, you can type something like "selected selected and 33" to add residue 33 to your selection. You can also select multiple parts of the structure in a single command like "select (42, 67, 82) and side chain and _C", which would select all carbon atoms in the side chain of residues 42, 67 and 82. You can learn common selection command in this [http://cbm.msoe.edu/includes/modules/jmolTutorial/jmolSelect.html tutorial]. The complete set of selection commands is explained in the Jmol manual. | *Selecting multiple parts of the molecule: When using the menu to select, each new selection command cancels the old one. Using the console, you can type something like "selected selected and 33" to add residue 33 to your selection. You can also select multiple parts of the structure in a single command like "select (42, 67, 82) and side chain and _C", which would select all carbon atoms in the side chain of residues 42, 67 and 82. You can learn common selection command in this [http://cbm.msoe.edu/includes/modules/jmolTutorial/jmolSelect.html tutorial]. The complete set of selection commands is explained in the Jmol manual. | ||
*Showing hydrogen bond: Select the entire structure or parts you are interested in (e.g. "select backbone and helix"), then type "hbonds calculate" in the console. This will calculate possible hydrogen bonds and display them. | *Showing hydrogen bond: Select the entire structure or parts you are interested in (e.g. "select backbone and helix"), then type "hbonds calculate" in the console. This will calculate possible hydrogen bonds and display them. | ||
</StructureSection> | |||
==External links== | ==External links== | ||