Z-matrix builder


            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  and  allow 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 automatically”.