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Structure Preferences: Drawing


How it works...

Double Bond Width (Pixels)

Allows you to specify the distance between double bonds. It only takes effect on printing.

Pen Width (Pixels)

Allows you to set the thickness of bonds. It only takes effect on printing.

Grid Spacing (mm)

Allows you to specify the default distance between grid lines. The Grid box must be checked for the Grid to be displayed. The grid is most useful for drawing when grid spacing either corresponds to a fraction of bond length or is equal to bond length.

Compass Interval (deg)

Allows you to specify the default compass interval.  Bonds drawn from an atom automatically snap to these compass intervals when the Snap Bonds option is checked.

Note that compass intervals used should be factors of 90 degrees (e.g., 15, 30, etc.); otherwise bonds cannot be drawn horizontally and vertically.

Bond Length (mm)

Allows you to set a default bond length which is used for the ring and chain commands and for 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 fixed length. Bonds are also then drawn to the nearest specified compass position.

Browse Delay (secs)

Allows you set the time between displays when browsing structure queries.

Atom Selection

This changes the display for the selection of atoms in the Draw menu and the Current Atom box (activated by a left click).

Dialog Box

The default dialog for atom selection is displayed on the left and all other elements are displayed in alphabetical order.

Periodic Table

Elements are displayed in a periodic table.


Elements, shortcuts and other variables are listed in a scroll box. Values can also be entered using the keyboard.

Note - A right click on the Current Atom box will open with the List option.


Dots - Causes carbons to be displayed and printed as a fat dot.

Angles - Causes carbons to be displayed and printed as an angle.

C’s - Causes carbons to be displayed and printed as C.

  Note - Carbon display for individual nodes can be changed by pre-selecting the nodes and clicking on the appropriate command in the Display menu. The Display menu feature is not related to Carbon display button on the toolbar or the Carbons preference.

Reaction Help

When this option is checked, help dialogs are provided when the Reaction Role and Reaction Site Tools are initially selected. This option is recommended when drawing reaction queries.


Turns a grid on which may act as a guide when drawing a structure. The grid line spacing can be changed using the Grid Spacing option.

Ring Circles

Draws circles inside normalized rings (replacing the alternating single and double bonds).

Note that refreshing the screen display is slower when ring circles are displayed, so it is faster to draw structures with this option unchecked and then check it before printing.

Snap Bonds

Allows you to specify the bond length that will be used for drawing rings and chains. Bonds drawn freehand will automatically snap to the nearest compass interval at the bond length that you specify. If this option is unchecked the standard bond length built into the program will be used for drawing rings; chains and bonds drawn freehand will be drawn using the length and orientation indicated by the cursor position.

Delete Atoms with Bond

Allows you to specify that the atoms at either end of a bond will be deleted when a bond is deleted, assuming there are no other attachment to the atoms.


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