Chemcraft provides different possibilities to build molecules and
change their geometry, which are useful for preparing an initial
approximation for computations, and other purposes. In many cases, a
molecule can be easily built using standard molecular fragments (see
Working with molecular fragments).
If two atoms are selected, pressing Ctrl+B inserts or removes a bond
between them. To alter the type of a bond (e.g. to make a bond dotted),
double left-click on it.
One can modify any geometrical parameter (bond length, bond angle,
dihedral) using the textbox at the bottom of the main window. When one
selects 2, 3 or 4 atoms, the value of corresponding parameter is shown in
the textbox. Attention must be paid to the sequence in which the atoms are
selected. If one modifies the value and presses Enter or the "set"
button, the positions of atoms are adjusted to the new value. Either the
coordinates of last selected atom will change, if the button
pressed, or the coordinates of first and last selected atom will change
symmetrically with the button
Other atoms bonded to the selected ones will move along with them, so it is
often important to insert or remove bonds, before changing a geometrical
parameter, via Ctrl+B. Specifically, the coordinates of all atomic groups
bonded to last (first) selected atom (i.e. directly bonded, not through
intermediate second/third selected atoms when changing angle/dihedral) but
not directly bonded to opposite first (last) selected atom, will be changed
(the coordinates of these atoms would be translated in parallel with last
(first) selected atoms, when a distance is changed, or rotated along
second/third selected atom together with last (first) selected atom, when an
angle/dihedral is changed). Pressing Ctrl+E moves the focus to the textbox
with the value of current geometrical parameter.
The program allows the coordinates of atoms to be changed by
"dragging" them using the mouse. The atoms or fragments are
"dragged" in dragging mode toggled by the "Edit/Drag
atoms" menu item or the button
Three submodes of the dragging mode can be used:
Drag individual atoms,
: clicked atoms are
moved in X or Y directions with the mouse. Pressing Num2/Num8 or Num1/Num3
(while the left mouse button is pressed) moves the atom in Z direction (in
parallel with the view orientation);
: individual radicals
(bonded groups of atoms, enclosed by the clicked atom and not including the
largest of these groups, which is considered by the program as the outer
molecule) are dragged and rotated, keeping constant the bond length, by
which the fragment is connected with outer molecule. Pressing Num2/Num8
moves the fragment in Z direction; pressing Num4/Num6 rotates it along the
bond connecting it with outer molecule; Num7/Num9 shortens/lengthens this
: whole molecules
(bonded groups of atoms connected with clicked atom) are dragged. Pressing
Num1-Num9 moves the group in Z direction or rotates it.
For the last two modes, the bonds in molecule determine the atoms to
be dragged together with the clicked atom, so it is often needed to add or
remove bonds via Ctrl+B before using these modes.
A group of atoms can be also rotated along the axis, defined by two
selected atoms, via "Edit/Rotate along selected" menu item. This
opens a window with a scrollbar, which rotates the atoms bonded with second
In some cases, it is helpful to perform complex geometry
modifications using the Console Editor ("Tools/Console editor"
menu item). It provides an iterative algorithm for applying new values for
an arbitrary set of geometrical parameters. The values of parameters are
entered in text mode (e.g. "r(1-2)=2.1, a(3-2-1)=120,…").
If an undesired change of coordinates is made, Ctrl+Z can be used.