Middle panel: shows an animation of the behavior of the system. To begin / stop the simulation, press the / stop” “start button. To go thru the simulation of discrete time steps, press the forward or backward arrows adjacent to the “slowly” start / stop button. Bottom not shown unless select in the tool panel. “properties” Left panel: not shown unless select in the tool panel. “plot” Mouse The mouse will be used to navigate the software. Unless stated otherwise, use the mouse button to select left various items. To move the content in the animation, mouse button to select the image, hold, then move the mouse. right-click To enlarge / shrink the image in the animation, rotate the mouse wheel. To rotate the image, select, hold, then move the mouse. To focus on a small region near a molecule: on a molecule, select clipping center”, then rotate right-click “set mouse wheel to magnify the image. To undo, on the expanded image, select clipping center”. right-click “unset Drop-down menu The content in this primer will not be comprehensive, so feel free to explore. Style the top 5 items (i.e. controls how the molecule is wire, ball & wire, tube, ball & spokes, space filling) displayed. to visualize H-bond IMF as a yellow dashed line H-bonds: generates a upon of collision of a molecule with another molecule and / or the Collisions: “flash” container wall, which make it easier to visualize molecular collisions. Alternatively, look for sudden changes in a molecule’s trajectory. shows the trajectory / path of the molecules in the simulation; to see the path of a Trails: all single molecule, select it before selecting “trails” choices: translational KE, intermolecular energy, or dipole moment. Color by property: use when viewing proteins; choices: monochrome, by secondary structure, by strand, by Ribbons: residue Snapshot
Middle panel: shows an animation of the behavior of the system. To begin / stop the simulation, press the “start / stop” button. To go “slowly” thru the simulation of discrete time steps, press the forward or backward arrows adjacent to the start / stop button. Bottom not shown unless select “properties” in the tool panel. Left panel: not shown unless select “plot” in the tool panel. Mouse The mouse will be used to navigate the software. Unless stated otherwise, use the left mouse button to select various items. To move the content in the animation, right-click mouse button to select the image, hold, then move the mouse. To enlarge / shrink the image in the animation, rotate the mouse wheel. To rotate the image, select, hold, then move the mouse. To focus on a small region near a molecule: right-click on a molecule, select “set clipping center”, then rotate mouse wheel to magnify the image. To undo, right-click on the expanded image, select “unset clipping center”. Drop-down menu The content in this primer will not be comprehensive, so feel free to explore. Style the top 5 items (i.e. wire, ball & wire, tube, ball & spokes, space filling) controls how the molecule is displayed. H-bonds: to visualize H-bond IMF as a yellow dashed line Collisions: generates a “flash” upon of collision of a molecule with another molecule and / or the container wall, which make it easier to visualize molecular collisions. Alternatively, look for sudden changes in a molecule’s trajectory. Trails: shows the trajectory / path of the all molecules in the simulation; to see the path of a single molecule, select it before selecting “trails” Color by property: choices: translational KE, intermolecular energy, or dipole moment. Ribbons: use when viewing proteins; choices: monochrome, by secondary structure, by strand, by residue Snapshot
odyssey_V5_primer.docx