Using Chemtool


Chemtool is a program for drawing organic molecules. It runs under the X Window System using the GTK widget set.

Most operations in chemtool can be accomplished using the mouse - the first (usually the left) button is used to select or place things, the middle button modifies properties (e.g. reverses the direction of a bond), and the right button is used to delete objects.

The program offers essentially unlimited undo/redo, two text fonts plus symbols, seven colors, drawing at several zoom scales, and square and hexagonal backdrop grids for easier alignment.

Drawing of bonds:

Bonds can be drawn in 4 different angle settings - hexagon with 30 degree intervals, two pentagons with 72 degree intervals (in different orientations), and a 45 degree octagon). Intermediate angles are possible in all of these modes as well - just ignore the marker points in this case.

Pressing the first (left) mouse button sets the starting point of a bond and also displays a set of markers at the appropriate angular positions. Dragging the mouse while holding down the button draws a line in the desired direction.

The bond style chooser in the center of the button bar determines the type of bond that is drawn - initially, this is a single bond. If you want to change the type of a bond later, either click on it with the middle button of your mouse to advance to the next type(s), or select the appropriate type in the chooser and then switch to bondtype mode and pick all bonds that you want to change over to the new type. Pressing the middle mousebutton on a bond when in 'Bondtype' mode reverses the direction of that bond.

The bond types available in chemtool are

The additional bond type available in the pulldown menu, is special insofar as no other bond type can be converted to or from this type. (it is actually a shortcut for one of the curve-drawing functions described below).

Pressing the third (usually the right) mouse button deletes the bond next to the cursor position.

Semiautomatic drawing of rings:

Rings of 3 to 12 members can be drawn easily by holding down the Ctrl key while drawing a line. This line will then become the first segment of a ring that is automatically drawn in clockwise direction. The size of the ring defaults to that appropriate for the selected drawing mode (i.e. 5, 6 or 8 sides), but it can be set on a per-ring basis by pressing Ctlr- before drawing the ring, where numbers 3-9 correspond to 3 to 9-membered rings, while 0 to 2 select 10, 11 and 12-membered rings, respectively. Newly drawn rings can be deleted by pressing Ctrl and mouse button 3 together.

Drawing of curved lines:

Curved lines for objects like arrows or orbital lobes can be drawn in spline curve mode by specifing four control points that form a bounding polygon (startpoint, two points on either side of the peak, endpoint). Of the regular bondtypes available in the Style menu, the 'single line', 'semiarrow', arrow and 'dashed line' retain their usual function, while the 'wide line' type is used to denote a filled polygon. The control points are only visible in 'Move' mode, where they can be dragged around to change the form of a curve after it is drawn.

For drawing curved arrows, there is also a predefined function in the bond style chooser. This is actually a shortcut for one of the curve drawing functions described above, with the second and third control points automatically generated. As such, it can not be converted to or from any of the conventional bond types.
(One can, however, convert it to any of the other curve types, e.g. to change the type of arrowhead). The shape of the arrow will usually need to be adjusted by shifting the control point that appears alongside it in 'Move' mode.

Inserting text:

Text written into the text box can be positioned with the cursor and may appear left, middle or right-aligned in the drawing. The font size can be selected from the chooser to the right of the text entry field, while the 't/T' button next to the text-alignment buttons lets you switch between two fonts - Helvetica for regular labels, and Times Roman for descriptions. Like the line drawings, text can be in any of the colors available on the color selector. If you want to change the color, font or alignment of a label afterwards, just choose the appropriate combination of settings and then select the desired label with the left mouse button. When the text entry area is empty, this will just update the properties without changing the text itself. When the text entry area is not empty, its contents will also replace the text of the label. Copying the text of a label to the entry area is done with the middle mouse button, while the right mouse button deletes the selected label.

There are two special characters to be used for sub- and superscripting the following character:

  '^'  to shift up (e.g. N^+ for N+)
  '_'  to shift down (e.g. CH_3 for CH3)

The control character '|' is used to itializise the following character, as in |t-Bu (t-Bu), while the '#' character boldfaces it.

The special character '@' switches to symbol mode, which uses the standard X11 symbol font. All alphabetic keys produce the corresponding greek characters in this mode, and several other symbols are available if their standard latin1 equivalents are already mapped onto the keyboard: