Drawing of bonds:

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. (The color used for the bond is updated at the same time if necessary.) Pressing the middle mousebutton on a bond when in 'Bondtype' mode reverses the direction of that bond.

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

The available bond types are:

Semiautomatic drawing of rings:

Newly drawn rings can be deleted by pressing Ctrl and mouse button 3 together.

Drawing of curved lines:

Setting bond style

The additional bond type available in the pulldown menu,

is only available for drawing. It 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

The control character '|' is used to italicise the following character, as in |t-Bu.

A bold fonttype, typically used for numbering compounds, can be selected by preceding the character with a '#'.

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:

The symbols 'plusminus' and 'registered' (trademark) are already in the standard font, although they are not normally available on the keyboard. Use the following commands (or add the declarations to your .xmodmaprc ) to make them available via <AltGr>+<Key> (<RightAlt>+<Key>):

(this leads to AltGr-P = plusminus, AltGr-R = registered in normal mode and AltGr-O = infinity, AltGr-U = uparrow, AltGr-D = downarrow in symbol font).

For 'dots-and-crosses' diagrams, the following mappings to the symbol font might be useful: acute -> cross (e.g. keysym x = x X acute) middle dot -> filled dot (e.g. keysym d = d D periodcentered) (using the degree sign for the open dot).

Circled versions of the plus and minus signs for denoting ionic charge are available as @+ and @- .

When you want to use symbols as sub- or superscripts, place the sub- or superscripting character before the '@' character, e.g. K_@a .

In text mode, the right mouse button deletes the label at the cursor position. Changing the size, font or color of a label can be done by left-clicking on it after choosing the desired combination of settings. When the text entry box above the drawing area is empty, only the settings are updated without changing the contents of the label, otherwise the label text is replaced as well. If you want to copy the text of an existing label to the text entry box, click on it with the middle mouse button.

Labeling shortcuts

The keys 'c','h','n','o','s','p' and 'r' insert the corresponding capital letter, 'l' (lowercase L) inserts 'Cl', while '1', '2', '3' insert CH,CH_2 and CH_3, respectively. The asterisk key (*) inserts a filled circle.

Pressing the space bar once allows you to enter arbitrary labels, which will be placed at the current position when you press the Return key.

Drawing electron pairs

Numbering atoms

Centering

Exporting to foreign formats:

You can create the outputs in different sizes according to the current zoom scale. Postscript and PicTeX files can also be created at arbitrary scales selectable on the export file menu.

An option in the configuration menu can be set to call fig2dev in international language mode, which will automatically render any text written in the alternate (Times) font using the postscript font appropriate for the current locale (currently Croatian, Cyrillic, Czech, Hungarian, Japanese, Korean, Polish). See the fig2dev documentation for details.

To include the PicTeX-file in your LaTeX document, you will need the pictex macro package. Depending on the versions you use, you might also have to load the 'color' package in the preamble of your LaTeX file. If you experience 'TeX capacity exceeded' error messages, increase the extra_mem_bot parameter in your texmf.cnf file (usually in /usr/share/texmf/web2c, /usr/local/texmf or /etc/texmf). Pictex is known for its unusual (by tex standards) memory requirements, and the standard settings do not account for this (although you may find a comment a la 'change this if you use pictex' in the texmf.cnf file). Something like extra_mem_bot=400000 should not hurt on any moderately modern system.

Printing drawings

Selecting all or parts of a drawing for transformations:

If you need to add atoms outside of the rectangular area to your selection, simply draw another rubberband around them while holding down the Ctrl key.

The selected parts will appear highlighted in blue and are immediately available for

moving

simply drag the fragment to the desired position with the mouse while holding down the left mouse button. (If you only need to move individual atoms or bonds, you can simply pick and drag them in 'Move' mode without having to mark them first).

rotating

horizontal movement of the mouse translates to smooth rotation around the pivot point selected when pressing the mouse button

flipping

(mirroring) the fragment about a horizontal or vertical mirror plane through its center: this is performed by clicking on the appropriate menu button

copying

clicking on the 'Copy' menu button creates an exact copy of the selected fragment slightly offset to the original. The mark is automatically transferred to the new copy.

rescaling

horizontal mouse movement is translated into a smooth increase or decrease of size of the marked fragment

deleting

to delete the marked fragment, simply click the third (usually the right) mouse button after it is highlighted.

framing

choosing one of the icons from the drop-down list of frame and bracket styles draws the corresponding object, e.g. a pair of round parentheses, around the highlighted fragment.

optimizing

clicking on the 'bucket and broom' symbol invokes a function that removes overlapping (duplicate) bonds and labels from the drawing and straightens lines that are almost horizontal or vertical.

Adding previously saved figures:

If you want to add it to a predefined position on another molecule, you can mark that attachment site by left-clicking on it instead of dragging the marker rectangle. A small green dot will appear at what is now the reference position for the new part. If you save molecules with such a marker set, it will in turn define their attachment site when they are added to another drawing.

Adding one of the predefined templates:

The data in the template system differ from normal chemtool drawings only by the fact that they are stored within the program, and in a slightly awkward format (x and y coordinates listed separately in the source file templates.h). These are meant to provide a convenient basis set available to all users, but not individually extendable (you can use the 'Add' function for your own structures). Please let us know if you want specific molecules added to the templates - their name or ideally a regular chemtool drawing file is all we need. (send email to martin@ruby.chemie.uni-freiburg.de)

Importing foreign file formats:

As both are 3D file formats, while chemtool only handles 2D projections, imported molecules are read into a temporary storage at first and displayed in blue on the canvas. This 3D representation can then be rotated using the mouse. Only after pressing the Return key on the keyboard is it converted into the final 2D projection that can be edited. While such a 3d import is in progress, all normal drawing and editing functions are disabled.

With MDL molfile import, the carbon atom labels are automatically discarded. For PDB import, the amount of labeling can be chosen in the file selection dialog, which offers retention of either all labels, only those of non-hydrogen atoms, or only the non-numeric part of the labels.

If the program babel is installed - either the original version written by Pat Walters or the more recent OpenBabel effort - chemtool will automatically offer a menu option for importing from any of the file formats this supports.

Determining sum formula and molecular weight:

Drawing functions not available within Chemtool: