User:Karsten Theis/sandbox: Difference between revisions
No edit summary |
No edit summary |
||
| (9 intermediate revisions by the same user not shown) | |||
| Line 6: | Line 6: | ||
<StructureSection load='' size='500' side='right' caption='Caption for this structure' scene='79/797412/Overall/1'> | <StructureSection load='' size='500' side='right' caption='Caption for this structure' scene='79/797412/Overall/1'> | ||
Here is scene three: <scene name='79/797413/A_la_irving/3'>BPG bound to hemoglobin</scene>, homage to Irving Geis. | |||
</StructureSection> | </StructureSection> | ||
<scene name='78/781027/Panela/3'>Panel A:</scene> | |||
==Basic reading and viewing== | ==Basic reading and viewing== | ||
| Line 15: | Line 18: | ||
*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. 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. 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? | ||
Change to <scene name='79/797412/Carb/ | Change to <scene name='79/797412/Carb/1'>detailed view.</scene> | ||
==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 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. 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. | *Identifying 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. 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. | ||
*Pressing 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. If your screen is touch-sensitive, you can also zoom with the usual two-finger pinch gestures. To move ( | *Pressing 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. If your screen is touch-sensitive, you can also zoom with the usual two-finger pinch gestures. To move (fingers. After you moved the molecule, it will still rotate around the old center of rotation (later we'll discuss how you can use the menu to change the center of rotation). | ||
*If you get lost: Sometimes, after zooming or rotating, the molecule is gone, or you loose your bearings. To get back to the original view, press the green link again. | *If you get lost: Sometimes, after zooming or rotating, the molecule is gone, or you loose your bearings. To get back to the original view, press the green link again. | ||
*Measuring: To measure distances, angles and torsion angles, you start by double-clicking an atom. For a distance, you just double-click a second atoms, and the distance appears. Repeating the process will erase the distance measurement. For angles, you need to define three atoms, with a double-click, click, double-click sequences. For torsion angles, you might have guessed it, you need four atoms (double-click, click, click, double-click). If you clicked on the wrong atom midway, click on an empty space to cancel. | *Measuring: To measure distances, angles and torsion angles, you start by double-clicking an atom. For a distance, you just double-click a second atoms, and the distance appears. Repeating the process will erase the distance measurement. For angles, you need to define three atoms, with a double-click, click, double-click sequences. For torsion angles, you might have guessed it, you need four atoms (double-click, click, click, double-click). If you clicked on the wrong atom midway, click on an empty space to cancel. | ||
translate) the molecule, press shift, double-click and drag. If your screen is touch-sensitve, you can also drag with two | |||
Change | Change tohttp://proteopedia.org/wiki/index.php?title=User:Karsten_Theis/sandbox&action=edit <scene name='79/797412/Overall/1'>opening scene.</scene> | ||
| Line 52: | Line 55: | ||
<scene name='79/797413/Sand/1'>1: Load molecule 1H6M</scene> | <scene name='79/797413/Sand/1'>1: Load molecule 1H6M</scene> | ||
<scene name='79/797413/Sand/2'>2: Load 1, Save with reload checked | <scene name='79/797413/Sand/2'>2: Load 1, Save with reload checked</scene> | ||
</scene> | |||
<scene name='79/797413/Sand/3'>3: Load 2, Save with reload not checked</scene> | <scene name='79/797413/Sand/3'>3: Load 2, Save with reload not checked</scene> | ||
| Line 61: | Line 64: | ||
<scene name='79/797413/Sand/6'>6: Load molecule 1HEW</scene> | <scene name='79/797413/Sand/6'>6: Load molecule 1HEW</scene> | ||
<scene name='79/797413/Sand/7'>7: Load Image:Aln 1H6M to 1HEW 2.pdb</scene> | |||
<scene name='79/797413/Dpg/1'>Hemoglobin DPG</scene> | |||
<scene name='86/865933/As_no_cartoon_labels_hbonds/1'>show hydrogen bonds</scene> and <scene name='79/797413/As_no_cartoon_labels_hbonds/1'>version 2</scene> | |||