The menu items in Book 3 all require atom picking. Generally, atoms are picked by placing the cursor at the atom and clicking the LMB. If the pick has been successful, a 'pick' noise will be heard. Use RESET (Book 8) to cancel any half-completed actions. ALL DISTANCES ARE IN ANGSTROMS AND ANGLES IN DEGREES.
Click 'Distance'. It will vanish. Click on the two atoms in turn for which you want the separation distance. After the second click, this distance will appear in the display zone and in the Text Port. The 'Distance' button re-appears and the process may be repeated- listing the distances as it goes. The display screen output will disappear if you decide to rotate the picture. A more permanent record is built up in the Text Port.
Angles are measured in the same way, but by picking more atoms.......
Planing molecules, for consistency of display particularly before writing them to disk, can be very useful. Planing is done on 3 chosen atoms.
Clicking this button will bring a little yellow information label up at the bottom left hand corner of the display. Pick three atoms. The final planed result will follow the information- i.e. the 1st atom picked will be 'down'. The 2nd will be on the left of the display (as you look at it) and the 3rd will be on the right.
These work in the same way as XY Plane. The yellow instruction will tell you the final orientation.
The perpendicular height of an atom above, say, a benzene ring, is often useful for designing pharmacophores. Click this button and follow the yellow instructions at the bottom left hand side. First, pick 3 atoms defining a plane (e.g. three atoms in a benzene ring). Second, pick the atom whose perpendicular distance above this plane you want to measure. The result is written both on the screen and in the Text Port. The 1st three numbers are the atoms defining the plane. The 2nd number (after the '/') is the atom number you picked to measure. The distance follows.
You can go on picking atoms to measure above the plane until you click on the yellow instruction (as it says!)
* Click on the * at the top left hand side of Book 3 for page 2.
Clicking this activates a question in the Text Port. Enter 'M' or default to define the centre of mass of the molecule or 'C' to define the centre of charge. After hitting <Enter> at the keyboard, the 'Centre' will appear as a brown point, linked to the nearest heavy atom it can find. The 'Centre' is defined as a 'dummy' atom with an atomic number of 0 (zero). Dummy atoms can be removed in Book 5.
These Centres can be used for generic measurements, overlay points and planing centres. They are often quoted in the literature as measuring points for spectroscopic or other experimental data.
The centroid of any combination of atoms can be represented (by a dummy) by picking the desired atoms and finishing the list by clicking on the yellow 'Touch here' label at the bottom of the screen. If you want to find the centroid of the entire molecule, click the Right Mouse Button (RMB) anywhere in the display after picking 'Centroid' in the menu. The centroid appears as a brown point linked to the nearest heavy atom.
Normals are useful to align complex groups and cycles. After picking the 'Normal to Plane' button, pick 3 atoms in the chosen plane of the normal. Then pick the atom onto which the normal will be constructed.
It is often useful to construct a normal at the centre of a ring. There is no atom here to do this with! - A tip is to create a centroid for the ring and use this from which to project the normal.
