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Structure Drawing Plug-in: Preferences Menu

Click a tab to see options for changing preferences. For other options that govern the display of structures, see the Display menu.

Chemistry

Check or clear a box to:

  • Show/hide Hydrogens.

  • Set Bond Default to Exact (this should always be checked).

  • Show/hide Reactions (show/hide reaction roles).

  • Set Query Mode. (click to clear the check box to change to Attributes mode. See QueryDef menu.

Layout

Change the appearance of the main window by repositioning (or hiding) the Toolbar, Tool Palette, and status bar. You may also change the language of the interface - if this option is available at your site.

Save Time

Enter a number to indicate the number of seconds to elapse before the Structure Drawing program saves the drawing. You also have the option of saving your drawing in PostScript format.

Warnings

From the list of warnings, select any that you would like to disable. All warnings are enabled by default. If you disable a warning, the warning will not appear when you perform an action that would trigger the warning.

Colors/Fonts

Select the colors and fonts to be used in drawings.

Drawing

Set values or select preferences that govern the way structures are drawn in the window:

  • Double Bond Width (Pixels) - adjust the spacing (in pixels) between the lines of a double bond. This applies only to printing.

  • Pen Width - Adjust the thickness of bond lines. This applies only to printing.

  • Grid Spacing - Specify the distance between grid lines. Grid spacing should correspond to a fraction of bond length or be equal to bond length. If this option is not available, check the Grid box at the bottom of the window.

  • Compass Interval - Specify the interval (in degrees) to which bond angles are drawn. For instance, if the compass interval is set to 30, then bond angles will be drawn at 30°, 60°, 90°, 120°, and so on.

  • Bond Length - Set a default bond length which determines the length of ring and chain bonds, as well as the bond length in freehand drawing when the Snap Bonds option is checked. Snap Bonds must be checked to set values for Bond Length. When a value has been set for Bond Length, all freehand bonds are drawn to that length.

  • Browse Delay - Set the duration of time between display of structure records when browsing a database.

  • Atom Selection - Set the atom selection to Dialog Box, Periodic Table, or List (scroll list).

  • Carbons - Set appearance of carbon atoms to Dots, Angles, or C's. You can also change the display of Carbons by selecting the Carbons option on the Draw menu after selecting a node.

  • Grid - Turn on grid.

  • Ring Circles - Draw circles inside benzene rings instead of alternating single and double bonds.

  • Snap Bonds - When this option is checked, bonds drawn freehand will snap to the nearest compass interval and be drawn to the length specified by Bond Length.

Structure Drawing Menus

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