Desmond Tutorial

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