Desmond Tutorial

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Desmond Tutorial Visualization and Analysis using Maestro Figure 8.1 Launching the Trajectory Player Click the ‘T’ button to open the Trajectory Player. 3. Click the T button to open the Trajectory Player. The Trajectory Player is shown in Figure 8.2 and the associated Maestro Workspace view can be seen in Figure 8.3. The Trajectory Player has two sets of options for frame control and display properties; the best way to learn about these options is to experiment with them. The Trajectory Player is fully documented in the Schrödinger Desmond User Manual listed in “Documentation Resources” on page 97. NOTE In most cases you do not want the entire system to be displayed when, for example, visually inspecting the conformational changes of a protein molecule along the trajectory. The Trajectory Player recognizes Maestroʹs current display settings, which means that you can select/deselect any set of atoms for display using the Display > Display > Undisplay Atoms menu options and you can also render the atoms in any way you want. The Trajectory Player will generate a smooth animation with your current display settings and you can even save it in an MPEG movie file for incorporation in any presentation material. Figure 8.2 The Trajectory Player Control the frame for the Trajectory Player with these options. Control the display of the Trajectory Player with these options. 82 D. E. Shaw Research September 2008
Visualization and Analysis using Maestro Performing Simulation Quality Analysis Figure 8.3 Workspace view for trajectory visualization Workspace view of the Trajectory Player. Performing Simulation Quality Analysis Maestro can also perform basic quality analysis. Launch this tool from the Applications > Desmond > Simulation Quality Analysis menu. The quality analysis window appears as shown in Figure 8.4. Figure 8.4 Simulation Quality Analysis window Select the energy file in this field. Click the ‘Analyze’ button. Results of the analysis appear in this area. September 2008 D. E. Shaw Research 83
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Desmond Tutorial Desmond Version 2.
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Preface Intended Audience This tuto
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from outermost to innermost, separa
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Contents Preface . . . . . . . . .
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Loading Files from the Command Line
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List of Figures Figure 1.1: Simulat
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1 Desmond Tutorial Introducing Desm
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Desmond Tutorial Tutorial Steps Fig
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Desmond Tutorial Tutorial Steps 3.
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Desmond Tutorial Tutorial Steps Sys
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2 Learning the Maestro- Desmond Env
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Learning the Maestro-Desmond Enviro
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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
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Page 69 and 70: 5 Finishing Preparations for Desmon
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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
Page 83 and 84: Preparing Free Energy Perturbation
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Page 97 and 98: 9 Analyzing Trajectories Using VMD
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Desmond Tutorial

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