Desmond Tutorial

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Desmond Tutorial Learning the Maestro-Desmond Environment Figure 2.1 Maestro window Maestro workspace Zooming In and Restoring Full View When you want to take a closer look at a portion of a molecular model, you can zoom in by right‐clicking a particular atom to center the view in that area and then scrolling the mouse wheel to zoom in or out. You can also zoom by pressing the middle and right buttons at the same time and dragging the mouse. Return to a full size view of the molecular model by clicking the Fit to Screen button in the main toolbar as shown in Figure 2.2. 20 D. E. Shaw Research September 2008
Learning the Maestro-Desmond Environment Visually Distinguishing Residues and Displaying Atom Infor- Figure 2.2 Returning to full screen view Click the ‘Fit to Screen’ button to restore a full view of the model. Visually Distinguishing Residues and Displaying Atom Information You can visually distinguish different residues, or display residue and atom information quickly, using the Sequence Viewer in Maestro. To use the Sequence Viewer, select Display > Sequence Viewer from the menu bar. The Sequence Viewer appears at the bottom of the window as shown in Figure 2.3. To highlight certain residues in the workspace, click the residue in the Sequence Viewer. To select more than one residue, use SHIFT‐click or CTRL‐click. The selected residues appear highlighted in yellow within the Workspace. To display information about an atom within the workspace, move the cursor over the atom. The corresponding residue and atom information is displayed just above the Sequence Viewer. Click in any empty space within the workspace to deselect your selections. September 2008 D. E. Shaw Research 21
Page 1 and 2: Desmond Tutorial Desmond Version 2.
Page 3 and 4: Preface Intended Audience This tuto
Page 5 and 6: from outermost to innermost, separa
Page 7 and 8: Contents Preface . . . . . . . . .
Page 9 and 10: Loading Files from the Command Line
Page 11 and 12: List of Figures Figure 1.1: Simulat
Page 13 and 14: 1 Desmond Tutorial Introducing Desm
Page 15 and 16: Desmond Tutorial Tutorial Steps Fig
Page 17 and 18: Desmond Tutorial Tutorial Steps 3.
Page 27 and 28: Desmond Tutorial Tutorial Steps Sys
Page 31: 2 Learning the Maestro- Desmond Env
Page 35 and 36: Learning the Maestro-Desmond Enviro
Page 41 and 42: 3 Preparing Proteins with Missing R
Page 43 and 44: Preparing Proteins with Missing Res
Page 55 and 56: 4 Preparing a Desmond simulation wi
Page 57 and 58: Preparing a Desmond simulation with
Page 69 and 70: 5 Finishing Preparations for Desmon
Page 71 and 72: Finishing Preparations for Desmond
Page 77 and 78: 6 Running Desmond Simulations Overv
Page 79 and 80: Running Desmond Simulations Running
Page 81 and 82: 7 Preparing Free Energy Perturbatio
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Preparing Free Energy Perturbation
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8 Visualization and Analysis using
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Visualization and Analysis using Ma
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9 Analyzing Trajectories Using VMD
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Analyzing Trajectories Using VMD Lo
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Analyzing Trajectories Using VMD Ge
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Analyzing Trajectories Using VMD Ge
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Analyzing Trajectories Using VMD An
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Analyzing Trajectories Using VMD Bi
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10 Documentation Resources Detailed
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