Advanced Playback Settings Dialog Box

Advanced Playback Settings Dialog Box Features

The features present depend on the suite you are using; the restrictions are given in the descriptions below.

• Define binding site radius as text box
• Display only option and section
  • Currently displayed atoms option
  • Atoms matching ASL definition option and controls
• Update secondary structure at each frame option
• Show simulation box option
  • Include vector lengths option
• Replicate system text boxes

Define binding site radius as text box

Set the distance from the ligand that defines the residues that are included in the binding site. A residue that has any atom within this distance of any atom on the ligand is included in the binding site.

This option is not present in the Materials Science suite.

Display only option and section

Display only the atoms that are specified by the options in the section. Reducing the number of atoms in the display can help you see the processes of interest. This option allows you more flexibility than the Hide atoms options in the Playback Settings Pane.

Currently displayed atoms option

Display only the atoms that are currently displayed. This option allows you to set up the display prior to playing the trajectory.

If you select this option, the Hide atoms options in the Playback Settings Pane are disabled (not applicable in the Materials Science suite).

Atoms matching ASL definition option and controls

Display the atoms that match the ASL expression in the text box. You can use the standard atom selection controls to select the atoms to display. If you already have a Workspace atom selection, the Load Selection button is active, and you can click it to obtain an ASL expression from the Workspace selection. The ASL expression is combined with the expression generated by the Hide atoms options in the Playback Settings Pane (with AND NOT logic), so that the atoms specified here are not shown if they are hidden by the Hide atoms options.

Update secondary structure at each frame option

Update the secondary structure assignment for each frame during playback. The ribbons are updated with any changes in secondary structure for each frame displayed. This option is selected by default.

Show simulation box option

Show the edges of the simulation box, in magenta. If you align or center the view on particular molecules, the simulation box moves around as the trajectory is played. This is because the molecule positions with respect to the simulation box change between frames. If the unit cell box for the entry is displayed (Unit Cell in the Workspace Configuration toolbox), it is hidden while the trajectory is played.

If you select Translate to first unit cell in the Playback Settings Pane, this option is automatically selected, and remains on even when you deselect Translate to first unit cell. It is also automatically selected for the Materials Science profile.

Include vector lengths option

Label the edges of the simulation box with the lengths of the lattice vectors for the box. These values can change during the course of a simulation, e.g. in the NPT ensemble, where volume is not conserved. This option is only available when you select Show simulation box.

Replicate system text boxes

Enter the number of replicas of the system to display in each of the three directions, in both the positive and negative directions. This enables you to visualize the movement across the simulation box boundaries. This option can add a large number of atoms in the Workspace, so you might want to limit the display so you can observe the process of interest.

If you include a reference entry in the Workspace after including the trajectory entry, these text boxes are disabled. You can replicate the system before including the reference entry, and the trajectory can be played with the replica and the reference entry as background. However it is recommended to always include the reference entry before the trajectory entry.

If the number of atoms varies between trajectory frames (as is the case for GCMC trajectories) these text boxes are disabled if you include a reference entry.