The menu item "Tools/Build Z-matrix/" allows a Z-matrix to
be generated in text format. Before using this feature one must first have a
structure of the molecule in Cartesian coordinates. In fact, this utility
allows one to convert molecular structure from Cartesian to Z-matrix
coordinates, not to build a new Z-matrix. For creating a new structure one
can use different possibilities of Chemcraft (see
Constructing molecules), or, for example, perform a calculation of geometry
optimization with a "cheap" method in Cartesian coordinates.
Each line in the Z-matrix defines one new atom and contains
information on its connectivity with previously defined atoms (a distance,
angle and a dihedral, formed by this new atom and three specified atoms).
When the Z-matrix Builder is activated, the user is prompted to
click on the atoms (at the main window) in sequence corresponding to desired
Z-matrix and specify some additional information concerning parameters of
the Z-matrix. The values of distances, angles and dihedrals are
automatically calculated by the program using the coordinates of the atoms
in the molecule.
Here is an illustration of using this feature. When the building of
Z-matrix starts, one must click on atom N1 to be placed at the first line of
the Z-matrix. Then one clicks on atom N2 forming the second line; any atom
in the molecule except the atom N1 can be clicked. After that, the atom
connected with atom N2 is clicked; for the second line that can be only the
atom N1. Then one should specify the type of parameter R(N1-N2) at the right
window: whether this distance is an independent parameter (in
"variables" section) or a fixed distance specified in the body of
Z-matrix (distances are usually chosen as independent parameters, except
some distances with dummy atoms). After the type of parameter is chosen in
the list and the button "Ok" is pressed, the atom N3 is clicked,
which will form the third line of Z-matrix, and
atoms N1 and N2 in any sequence, with which the atom N3 will form a
distance and an angle. The distance can be chosen as a fixed parameter, a
new independent parameter, or being equal to previously chosen parameter
R(N1-N2), if the types of atoms are the same. The angle can be chosen as a
fixed parameter or an independent parameter. For the fourth and subsequent
lines, the same actions should be performed specifying three parameters
(distance, angle, dihedral); additional menu at the top of the window allows
one to choose whether the last parameter is a dihedral or a second angle.
The type of current choice is indicated by the text line at the top of the
main window. The button "Finish" finalizes the Z-matrix
construction and shows it in separate window; the button "Show"
displays this Z-matrix without finishing its creation. The buttons
one to undo/redo the last choice of atoms and parameters (nevertheless, in
case of errors, if the Z-matrix is not clearly designed, it must be often
rebuilt from the beginning).
After pressing "Show" or "Finish", a form with
the generated Z-matrix is shown. The checkbox "Clean angles" at
the form checks whether values of angles and dihedrals close to standard
values (e.g. 90.0, 109.4712, 180.0, etc) are set equal to these values.
In some cases one should add dummy atoms to the current molecule
before activating this tool. If two or more atoms are selected,
"Edit/Insert dummy atom into center of selected" menu item places
a dummy atom into coordinates center of the selected atoms.
The button “Complete automatically” runs the automatic completion
of the Z-matrix created. This option can be useful with big molecules; if
you have a big molecule and want to build a Z-matrix with a specified
distance or angle, you should firstly define the initial part of the
Z-matrix containing the required distance/angle, and then press “Complete