This is a general purpose molecular structure viewing and analyzing program. A variety of available molecular structures recalled from disk may be viewed, rotated and analyzed for bond orders, bond lengths, bond angles and torsion angles. The program begins with a p-dichlorobenzene molecule in the viewing box, but there are many other molecules to view.
File Access
1. Click on Get File to retrieve a molecule. There are 7
categories of molecules from which one can choose.
Double click on any one of the following:
Amino acids (aminoacd)
Hydrocarbons (hydrocar)
Misc. Organic (miscorg)
Sugars (sugars)
Halocarbons (halocarb)
Inorganic (inorganc)
Nucleotides (nuctides)
Click on the molecule file you wish to view.
Molecule Movement
1. Click on the Rotate button to rotate the molecule. Place the
mouse pointer on the molecule, hold down the left mouse
button and move the mouse to move the molecule.
- Moving the mouse left and right will spin the molecule
around the y-axis (vertical on the screen).
- Moving the mouse up and down will spin the molecule
around the x-axis (horizontal on the screen).
- The sensitivity of molecule rotation to mouse movement
can be altered by adjusting the Sensitivity scroll bar.
2. To freeze the molecule in position, simply release the left mouse
button.
3. Selecting the Spheres option causes the atoms to be depicted as
spheres when the molecule is frozen.
4. Selecting the Atom Labels options leads to labels of the atoms
with atomic symbols.
5. To alter the size of the molecule in the viewing area, adjust the
Size scroll bar. The molecule will not re-size on the screen until
the molecule is rotated again.
6. To alter the perspective of the molecules, adjust the Perspective
scroll bar.
- When set to close, the portions of the molecule that are
"close" to the viewer (coming "out" of the screen) will appear
to be larger in terms of the room parts of the molecule occupy
on the screen.
- By setting Perspective to the most distant position, the
molecule appears rather flat and undistorted. A close setting
leads to a distorted view of the molecule. It is generally easier
to get a feel for the 3-dimensional shape of the molecule using
a fairly close Perspective setting.
Structure Analysis
1. Once the molecule is rotated into a good viewing position, analysis
is initiated by selecting the Query mode. The information will
appear at the bottom of the viewing window.
2. To access the Query mode, click on the Query option button.
3. To determine the Distance between two atoms, click on the two atoms
consecutively. The two atoms need not be bonded to each other.
4. To determine a Bond Angle, click on three atoms in succession.
Torsion Angles may be determined by clicking on four atoms
successively.
5. To examine a number of bond distances without getting bond and
torsion angles, simply click on any clear space in the viewing
window. This redraws the molecule and restarts the query procedure.
Printing
Simply click on the Print button to print a molecular structure.
