The settings in this windows are stored between invocations of 3dmod along with the user preferences, rather than in a model file. The settings are:

• Draw scale bars can be used to turn the scale bars on and off. Bars are drawn only this checkbox is on.
• Draw on all snapshots can be used to make sure that image snapshots have scalebars when Draw scale bars is checked, even if the dialog is not open. Otherwise, they are drawn only when the dialog is open. Another modification that may be desired for snapshots is to turn off the markers for the current point and beginning and end of a contour, and the red cross in the center of the slicer. This can be done with a preference in the Snapshots tab of the 3dmod options window.
• White bars can be turned on to get white rather than black bars. It is not necessary to turn this on to get a white bar in the Model View window, as long as an image is not being displayed there. In that case, when the Model View window has a black or a white background, the scale bar is automatically drawn as white or black, respectively, regardless of this setting. However, if image display is on, then the scale bar is drawn as black by default, and this checkbox can still be used to have it drawn as white.
• Vertical bars can be turned on to get vertical instead of horizontal bars.
• Color ramp can be used to get a false color ramp instead of a black or white bar. This bar provides a key when showing images or stored values with false color. The colors will be based on the standard false color map in 3dmod, or on a custom map if one was loaded.
• Invert ramp will reverse the direction of color ramp. Note that stored values are displayed with an inverted color ramp, while the false color ramp for image display can be inverted with the F11 hot key.
• Minimum length controls the size of the scale bars by specifying their minimum length in pixels. The smallest round number is found that gives a bar at least this long.
• Thickness sets the thickness of the bars in pixels.
• The Position combo box allows you to place the bars in any one of the four corners of a window.
• Indentation in X and Y determine the distance of the bar from the edges of the window and can be set to shift the bar farther away from the corner in either direction.
• When Make bar multiple of is turned on, the bars will always be set to the value in the spin box times a power of ten, rather than to a multiple of 1, 2, or 5. This feature can be used to get bars of intermediate length; for example, when a 20 nm bar is too short but a 50 nm bar seems too long.
• When Make bar exactly is turned on, the bars will always be set to exactly the value in the text box, overriding the setting of Make bar multiple of and regardless of the length in pixels. This feature is useful for keeping the bar to a fixed size in real units when making a series of snapshots (e.g., a movie in Model View) with a widely varying zoom. The first time this is turned on, it will use the last scale bar length drawn. This will be helpful if you get the bar to the desired size before turning this option on.
• When Draw labels is turned on, the length of the scale bar will be written below the bar. The font size can be set in the Size spin box, and the spacing between the bar and the label can be adjusted with the Y offset spin box. This offset can be negative to place the label above the bar. When taking a montage snapshot, the font and spacing will be scaled along with the scale bar so that the snapshot will resemble the current image when viewed at the same size.

Montage snapshots: You may need to adjust the scale bar properties if you want to take a high-resolution montage snapshot of the Zap or Model View windows. Scale bar size and indentation are automatically scaled up by the montaging factor so that the bar will appear proportionally the same in the snapshot as in the original window. However, this scaled up bar must be located entirely in one of the montage panels (e.g., in the bottom right quarter of the window if montaging by 4). If the bar does not fit in a panel with the properties that you have set, the program will first try to shift the bar toward the corner of the image by reducing the indentation in the direction of the bar length (X for a horizontal bar). If that change is not sufficient, it then tries to shorten the bar by reducing the minimum length of the bar in pixels to as little as half of the original setting. A message is printed indicating either that such changes were made, or that the bar cannot be drawn with the current settings. In the latter case, or if you do not like the changes that were made, you can adjust the settings yourself to position the bar completely within one panel.

In any case, the actual length of the scale bar for the montage is printed on the terminal, since it is possible for the length to be different from that in the original window.

Variable Pixel Sizes: When you run 3dmod with multiple files that have different pixel sizes, the scale bar will be based on the pixel size of the file currently being displayed, provided that the model has a pixel size defined with units other than "pixels". This applies when multiple single-image files are displayed as Z slices instead of as separate times. In addition, if pixel size varies within an image file and metadata from SerialEM are available, the scale bar will be based on the pixel size of the current section. Such metadata can be provided in three ways: 1) by having the ".mdoc" file associated with an MRC file present along with the MRC file; 2) in an HDF file; or 3) in an ".idoc" file describing a list of single-image TIFF files, if 3dmod is opened with the ".idoc" file.

There is one limitation to be aware of: the scalebar is based on the current time and section number of the program as a whole, so it will not be correct for a locked window displaying a section or time with a pixel size different from the current one. Help Index