Scale Bar

The Scale Bar tool draws a scale bar and associated label. Scale bars are often included in images for presentation and publication. Chimera has no inherent spatial units, so the scale is determined by the coordinates of the input data. While atomic coordinates are usually in angstroms, many other units (nanometers, microns, etc.) may be encountered, depending on the type of data. The state of Scale Bar is included in saved sessions.

There are several ways to start Scale Bar, a tool in the Higher-Order Structure category. Starting Scale Bar brings up a dialog for creating the scale bar.

Turning Show scale bar on creates and displays a bar according to the existing settings; turning it off deletes the bar. Deleting and re-creating the scale bar frequently resolves problems such as disappearance of the bar or label. The bar is a cylinder that exists in three dimensions.

Typed-in settings will not be applied until the Enter (return) key has been pressed. Length and Thickness are expressed in the current display units. The bar and label Color settings can be changed by clicking the respective color wells. The Label text is as shown in the adjacent field except that the Length value is substituted for every occurrence of the pound sign # (zero, one, or multiple times). The label Offset is the position of the bottom left corner of the label relative to the middle of the bar edge, in the current display units. Bar Orientation may be horizontal or vertical. When the bar is horizontal, the label Offset is relative to the top of the bar; increases in the two values move the label rightward and upward, respectively. When the bar is vertical, the label Offset is relative to the right side of the bar; increases in the two values move the label downward and rightward, respectively.

The Preserve screen position fields describe the horizontal and vertical positions, respectively, of the center of the bar within the graphics window. The horizontal value ranges from -1 to 1 going from left to right and the vertical value ranges from -1 to 1 going from bottom to top. Preserve screen position keeps the bar center at the indicated position when the view is scaled (of course, the bar is still scaled). When Preserve screen position is off, the bar can drop out of view when the view is scaled up.

When the bar is created with Show scale bar, or when one of the Orientation settings is chosen, the bar is made parallel to the XY plane (the plane of the screen). The ends of the bar have the same Z coordinate, where Z is the dimension perpendicular to the screen. When created with Show scale bar, the bar is placed halfway between the near and far clipping planes (these can be viewed and moved in the Side View).

When Move scale bar... is off, the data models are activated for motion and the scale bar is deactivated. Turning Move scale bar... on reverses these settings, so that the bar can be translated and rotated with the mouse while the other models remain fixed. After a scale bar has been moved around, its ends can have different Z coordinates (one end of the bar can be closer than the other), which is usually not desired. Clicking one of the Orientation settings is an easy way to bring the bar back parallel to the plane of the screen.

Two additional issues relate to the existence of the scale bar in three dimensions:

• Depth cueing. By default, the display is brightest at the front clipping plane and dimmest at the rear clipping plane. If the scale bar is too dim, there are two general ways to make it brighter:
  • the position of the scale bar relative to the clipping planes can be adjusted, by moving the scale bar or one or both clipping planes; the clipping planes can be moved using the Side View
  • depth cueing can be turned off or adjusted, using the Effects panel
• Perspective. By default, the display has perspective, such that nearby items appear larger than items that are distant. There are two general ways to ensure that scale is accurately depicted:
  • the scale bar can be moved to the same depth as the data (or the approximate average depth, since the data is generally three-dimensional)
  • the perspective can be turned off so that items appear the same size regardless of how far away they are, using the Camera panel (set projection to orthographic)

THE SCALE BAR IS A MOLECULE

The scale bar is implemented as a molecule model containing one residue, three atoms (two ends of the bar and one for label positioning), and one bond (connecting the end atoms). Thus, any actions or commands that affect the display of atoms and bonds can also alter the appearance of the scale bar. When the data models contain atomic coordinates (that is, when they are also molecule models), it may be best to adjust their appearance as desired for the final image before creating the scale bar.

Turning Show scale bar off and then back on will cure many ills. This actually deletes the scale bar (closes the scale bar model) and creates a new one in accordance with the settings in the Scale Bar dialog. When the scale bar is created, it is opened as the lowest available model number. The end atoms are undisplayed and the bond between them is represented as a stick (cylinder). Only one scale bar can exist at a time.

No control over label font and size.
The font type and size of labels cannot be changed.

Label text can turn out smaller in printed and saved images.
Label text is restricted to a certein height in pixels. When an image is saved or printed at a different resolution than the current screen display, the size of the label relative to the rest of the image will be different than it is in the display. Higher resolution of the saved or printed image corresponds to a smaller relative label size.

The label atom is sometimes visible.
As mentioned above, the scale bar is implemented as a molecule, with one of its atoms defining the location of the label. The label atom must remain displayed for the label to be displayed. When the scale bar is created, the label atom is colored to match the current background. If the background color is subsequently changed (see the Background Preferences), the label atom may be visible against the new background. Deleting and re-creating the scale bar with Show scale bar solves this problem by making the label atom match the new background color.