Dialog Box - called from: Atoms Dialog
With this dialog you can construct a molecule or structure fragment from a table of bond length and angles. The table, called a z-matrix, is widely used in molecular science, and you can read files in this form from other sources or write files for use in other software.
Action button section
The buttons at the top of the dialog indicate actions to be taken after the z-matrix at the bottom is filled out
Add will add the new generated atoms to the atoms already in the Atoms (Input) list. If the structure axes are not already Cartesian they are changed to Cartesian.
Replace will remove all the old atoms from the Atoms (Input) list and insert the new generated atoms.
Add and Replace will change the structure axes to Cartesian, since all calculations with z-matrices assume Cartesian coordinates, but most other settings, such as symmetry, boundary option and others in the Input1 menu, will not be changed
Read will read a file containing a z-matrix and insert the contents into this dialog. There should be no title or other extraneous lines, and each line, one line per atom, should contain the fields Label, Bond Connect, Bond Distance, Angle Connect, Bond Angle, Dihedral Connect and Dihedral Angle. Note that atom Type is not in this sequence, but the atom type or atomic number may be on the end of the line. The fields should be separated by spaces, commas, colons or semicolons.
Write will write a file as described in the previous paragraph, with one line for each atom, and with the type number at the end of the line. The Orientation (below) will be added after the atoms.
Show will do a conversion from z-matrix to Cartesian coordinates and display the z-matrix and the results in a Text window.
You can cut-and-paste blocks of atom lines in the z-matrix by using the Read, Write and Show buttons - for example you can save a file from the Text window (Show) after suitable editing, then Read it back.
Orientation section
The Orientation section allows the molecule or fragment to be located and oriented in any desirable way. It always refers to the first three atoms in the z-matrix list. Coordinates are always Cartesian.
The Position gives the x, y and z coordinates of the first atom. By default they are 0,0,0.
The Atoms 1-2 vector gives the vector from the first to the second atom. By default it is 1,0,0, which puts the second atom on the x-axis at the given bond distance from the first atom.
The Atoms 1-2-3 plane gives the normal to the plane containing the first three atoms. The vector from atom 2 to atom 1, the vector from atom 2 to atom 3, and this normal form a right-handed system. By default this normal is 0,0,-1 which puts the third atom in the x-y plane with a positive angle giving a positive y-coordinate for atom 3 (assuming standard placement and orientation for atoms 1 and 2).
The vectors need not be normalized; they will be normalized during the transformation.
Z-Matrix section
Each line in the matrix below refers to an atom. You can select each atom by clicking on the number to the left, and the entries are acted upon by the Move Up, Move Down (move the line within the list), Insert and Delete buttons. The up and down arrows to the right scroll the entire list up or down if there are more atoms than the list can hold at once.
The atoms are positioned with respect to other atoms in the list. The first three atoms are oriented and positioned as described above in Orientation, and all other atoms are placed with respect to these three.
Each line describes the positioning of a new atom (1) with respect to up to 3 atoms already in the list (2, 3, and 4).
The Label and Type give the ATOMS label and type; the type is normally the atomic number. If the type is 0, ATOMS will attempt to determine the atomic number (or other type number) from the first two characters of the label.
Bond Connect: the number in this list of the atom (2) to which the new atom (1) is directly bonded.
Bond Distance: distance in Angstroms from 1 to 2.
Angle Connect: the number in this list of an atom forming an ordinary angle 1-2-3.
Bond Angle: the value of the angle 1-2-3 in degrees.
Dihedral Connect: the number in this list of an atom forming a dihedral angle 1-2-3-4. The dihedral angle is the angle between the normals to the plane 1-2-3 and the plane 2-3-4. This angle (sometimes referred to as tau) is conventionally given values from 0 to 180 and 0 to -180 degrees, and the sign is positive if, viewing the angle along the bond 2-3, with 2 nearer the observer than 3, the angle from the projection of 2-1 to the projection of 3-4 is traced in the clockwise sense (definition from Wilson, Decius and Cross, Molecular Vibrations, 1955, p 60).
Dihedral Angle: the value of the angle between the normals to the plane 1-2-3 and the plane 2-3-4 in degrees.