Workspace Configuration Toolbox Features

Workspace Toggles section

This section provides toggles for displaying structure-based objects in the Workspace.

Alternate Positions

Show atoms that are alternate positions for existing atoms, as "ghost" atoms. These alternate positions come from crystal structures where a set of atoms occupy two different positions in the crystal, e.g. two rotamers of a protein side chain. You can switch between the two sets of positions—see Selecting Rotamers and Torsions

Unit Cell

Display the boundaries of the unit cell of any periodic structure in the Workspace.

Dipole Moment

Display the dipole moment of each molecule in the Workspace as an arrow, centered on the centroid of the molecule, with a length proportional to the value of the dipole moment. If the entry has a dipole moment property (for example, from Jaguar, QM dipole X/Y/Z), this dipole moment is displayed; if it does not, the dipole moment is calculated using the coordinates and atomic partial charges (generated using the default force field). The appearance of the arrow is controlled by preferences—see Dipole moment settings.

Coordinate Axes

Display the Cartesian coordinate axes of the structure in the Workspace. These axes rotate as you rotate the view. Note that the view axes always have x horizontal, y vertical, and z pointing out of the screen.

Moments of Inertia

Display the principal moments of inertia of each molecule in the Workspace, as a set of orthogonal tubes whose length is proportional to the moment in the direction of the tube. The moments of inertia are calculated from the masses and coordinates of the atoms when you request their display. The actual values for each moment are displayed in the Status bar when the pointer is over the tubes.

 

Workspace Gadgets section

This section provides toggles for showing windows in the Workspace that provide information or access to tools for interacting with the Workspace structure.

Clipping Planes

Display the clipping planes window, in the lower-right corner of the Workspace. This window shows a top view of the structure, with the planes that are used to clip the structure in the front and back, as well as the planes that show the clipping on the sides where the atoms are outside the screen view. See Adjusting the Clipping for more information.

2D Overlay

Display the 2D Overlay in the lower left of the Workspace. This pane shows the 2D structure of one of the smaller structures in the Workspace (such as ligands), with option to step through multiple structures.

Command Input Area

Display the Commands text area at the foot of the Workspace, for entering Maestro commands. See Command Input Area and The Maestro Command Language for more information.

Entries / Hierarchy

Display the Entry List / Structure Hierarchy panel on the left side of the Workspace. This panel shows the list of entries in the project, and the structure hierarchy of the Workspace structure.

Workspace Properties

Display entry properties of a Workspace entry as text in the upper right of the Workspace. See Displaying Entry Properties in the Workspace for more information.

Sequence Viewer

Display the Sequence Viewer at the foot of the Workspace, for interaction with proteins and other biopolymers in the Workspace through their residue sequences.

 

Workspace Layout section

This section provides tools for the layout and appearance of the Workspace.

Tile

Display each entry in the Workspace in a separate window, or tile. When the toggle is on, tools for controlling the tiling are displayed to the right. See Tiling the Workspace for more information.

Stereo

Display two images of the Workspace structure that can be viewed as a single stereo (3D) image with the help of a stereo viewing device.

Color

Select the background color of the Workspace from the choices presented.

Font Size

Increase or decrease the font size of the text in the Workspace with these buttons. See Fonts settings for more information.