Modify moleculeentry in the
Moleculesubmenu. The dialog box shown in the Figure is displayed. The upper part contains the periodic table of elements and allows the selection of the element to be added or used as replacement.
In the middle there are a number of buttons for selecting different operations
and certain defaults. These are the following:
If this item has been chosen atoms can be selected with the mouse and geometry changes carried out as described in the previous section.
An atom of the element selected in the periodic table will be attached to the atom in the molecule clicked on with the left mouse button. The new bond will have the bond order selected in the editor dialog box and a bond length which is 90 % of the sum of the atomic radii (read from the
viewmolrc file). The local geometry
of the atom clicked on will be changed to reflect the current coordination of this
atom (two bond partners - linear, three - trigonal planar, four - tetrahedral,
five - trigonal bipyramidal, six - octahedral, seven - pentagonal bipyramidal etc.).
An atom clicked on with the left mouse button will be deleted. If
changes local geometry is turned on the local geometry of the atom(s)
connected to the deleted one will be changed in the same way as described under
Add atom. Otherwise the local geometry remains as before.
The atom clicked on with the left mouse button is replaced by the element selected in the periodic table. Bond lengths are adjusted to reflect the new element as long as the atom changed is not part of a ring.
A new bond will be created between the two atoms clicked on with the left mouse button. This bond will have the order selected under
The bond between the two atoms clicked on with the left mouse button is deleted. Bonds created or removed by the user have precedence over bonds created automatically. This means that once a bond has been created by the user only the user can remove it and vice versa regardless of what happens to the molecule.
The bond between the two atoms clicked on with the left mouse button is assigned the bond border selected under
While building a molecule bond lengths of newly created bonds are set to 90 % of the sum of the atomic radii of the bonded atoms and bond angles are assigned according to the coordination. Torsion angles can be selected from this menu. Available values are trans (180o), cis (90o), gauche (60o), and -gauche (-60o). This allows the construction of more complicated molecules. The torsion angle is always measured along the backbone of a molecule, i. e. while building e. g. a hydrocarbon chain the torsion angle is always measured between the carbon atoms. The backbone of a molecule is determined by counting all atoms attached to one atom and following the bonds which connect the atoms with the largest number of other atoms attached.
This menu allows the selection of the bond order for bonds. Available are single, double, and triple. Bond conjugation and hydrogen bonds are determined automatically according to the respective settings in the
Bond type menu.
If an atom is deleted the local geometry of the atom(s) bonded to it can either be left unchanged or modified according to the new coordination. This switch can be used to select which behavior is preferred.
change which can be used to reverse all changes to the molecule
(except changes to bonds). The number of undos is unlimited.
Jörg-Rüdiger Hill Fri Oct 31 14:19:21 CET 2003
In the middle there are a number of buttons for selecting different operations and certain defaults. These are the following: