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Constructing molecules
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
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
Drag individual atoms,
Drag fragments,
Drag molecules,
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
selected.
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.
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