Jmol/Quaternions: Difference between revisions
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m User:Karsten Theis/quaternions moved to Jmol/Quaternions: add to other Jmol resources, let others edit |
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<StructureSection load='' size='340' side='right' caption='' scene='43/433638/Fullview_cartoon/ | <StructureSection load='' size='340' side='right' caption='' scene='43/433638/Fullview_cartoon/21'> | ||
==Examples of how quaterions are used== | ==Examples of how quaterions are used== | ||
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Jmol shows structures (e.g. atomic positions) on a display and allows the view to be rotated and individual atomic positions to be manipulated. The display has Cartesion coordinates (the x-axis goes right, the y-axis goes up, and the z-axis points at the viewer). The atoms have Cartesian coordinates x, y, z. The meaning of the axes is sometimes arbitrary (NMR structures) or along certain crystallographic directions (X-ray structures). When you rotate the model, the coordinate system of the model is rotated (same coordinates x, y, z, but axes of coordinate system point in different directions) with respect to the display coordinate system. | Jmol shows structures (e.g. atomic positions) on a display and allows the view to be rotated and individual atomic positions to be manipulated. The display has Cartesion coordinates (the x-axis goes right, the y-axis goes up, and the z-axis points at the viewer). The atoms have Cartesian coordinates x, y, z. The meaning of the axes is sometimes arbitrary (NMR structures) or along certain crystallographic directions (X-ray structures). When you rotate the model, the coordinate system of the model is rotated (same coordinates x, y, z, but axes of coordinate system point in different directions) with respect to the display coordinate system. | ||
<jmol><jmolButton><script>axes on</script><text>show axes</text></jmolButton></jmol> | <jmol><jmolButton><script>axes MOLECULAR; axes on</script><text>show axes</text></jmolButton></jmol> | ||
When a new structure is loaded, the model axes point left, up, and out of the screen. The Jmol command "reset" puts that coordinate system back into that initial orientation. | When a new structure is loaded, the model axes point left, up, and out of the screen. The Jmol command "reset" puts that coordinate system back into that initial orientation. | ||
<jmol><jmolButton><script>reset</script><text>reset to initial orientation</text></jmolButton></jmol> | <jmol><jmolButton><script>reset; axes MOLECULAR; axes on</script><text>reset to initial orientation</text></jmolButton></jmol> | ||
==Changing orientations using quaternions== | ==Changing orientations using quaternions== | ||
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Choosing x = 1, y = 0.5, z = 0 and tilt = 10, the buttons illustrate the commands. | Choosing x = 1, y = 0.5, z = 0 and tilt = 10, the buttons illustrate the commands. | ||
<jmol><jmolButton><script>s = quaternion(); r = quaternion({1 0.5 0},10); tilted = r * s; moveto 1 quaternion @tilted </script><text>tilt 10 degrees away from view</text></jmolButton></jmol> | <jmol><jmolButton><script>s = quaternion(); r = quaternion({1 0.5 0},10); tilted = r * s; moveto 1 quaternion @tilted </script><text>tilt 10 degrees away from view</text></jmolButton></jmol> | ||
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<jmol><jmolButton><script>q10 = @qr / 10; | <jmol><jmolButton><script>q10 = @qr / 10; | ||
moveto 0 quaternion q0;delay 0.5; | moveto 0 quaternion @q0;delay 0.5; | ||
qn = q10 * q0; moveto 0. | qn = q10 * q0; moveto 0.5 quaternion @qn; | ||
qn = (q10 * 3) * q0; moveto 0. | qn = (q10 * 3) * q0; moveto 0.3 quaternion @qn; | ||
qn = (q10 * 7) * q0; moveto 0.2 quaternion @qn; | qn = (q10 * 7) * q0; moveto 0.2 quaternion @qn; | ||
qn = (q10 * 9) * q0; moveto 0. | qn = (q10 * 9) * q0; moveto 0.3 quaternion @qn; | ||
qn = (q10 * 10) * q0; moveto 0. | qn = (q10 * 10.1) * q0; moveto 0.5 quaternion @qn; | ||
qn = (q10 * 10) * q0; moveto 0.5 quaternion @qn; | |||
</script><text>rotate all the way with variable speed</text></jmolButton></jmol> | </script><text>rotate all the way with variable speed</text></jmolButton></jmol> | ||