Volume 2 Chapter 5 Edit Menu BOND

Function

BOND allows the editing operations to be applied to an individual bond.

Remarks

The valid editing operations which can be applied to a bond are:

ADD
ROTATE
DELETE
SCALE

Examples

Suppose (i) is the starting fragment.

Select BOND
Select ADD

Use the cursor to select the BOND TYPE:
(Select another command to end this one.)

Select bond type DOUB

Select an ATOM at one end of the BOND
(Select another command to end ADD BOND)

Select atom a

Select the ATOM at the other end of the BOND
(Select another command to CANCEL ADD BOND)

Select atom b
Fragment is now (ii).

Select an ATOM at one end of the BOND
(Select another command to end ADD BOND)

Select DELETE

Use cursor to select BOND to be DELETEd
(Select another command to end DELETE BOND)

Select C - N bond
Fragment is now (iii).

Use cursor to select BOND to be DELETED
(Select another command to end DELETE BOND)

BOND ROTATE allows you to select a bond, and specify its angle to the horizontal. When you select BOND ROTATE, a compass is drawn at the top left-hand corner of the drawing area, and the angle in degrees of each bond to the horizontal is displayed at the centre of the bond in green, with an arrow head showing the bond direction.

The structure shown in (i) is on the screen.

(i)

ROTATE will be used to tidy up its bonds.

Select ROTATE
(i) appears in the drawing area.
You are then prompted:

Select the atom which will remain fixed:
(Select another command to CANCEL this one)

Select the central C atom
The atom you select is marked with a red cross.

Select the atom which will move:
(Select "CANCEL" if you don't want to ROTATE a BOND)

Select the C on the far right
The atom you select is marked with a red cross.
You are then prompted:

Use cursor on the compass to select the required angle to horizontal,
OR type the value and press <RETURN>

Type 0 <R>
The structure becomes as shown in (ii).
(ii)

By repeatedly selecting bonds and correcting their angles, you can tidy up a structure. The result after tidying up all the bonds in the structure in this example is shown in (iii).

(iii)

If there is no bond between the atoms the program will sound an alert and warn:

ERROR - There is no bond between those two atoms - Please try again
Select the atom which will remain fixed:(Select another command to CANCEL this one)

You can use the numeric keypad on Tek 4200 Series terminals to type the required angle, instead of using the cursor to select an angle, then press <ENTER> instead of <RETURN>. Using the compass, you can only select angles which are multiples of 30 degrees. By typing the number, you can select any integer.

If you do try to type the angle, and make a mistake, an alert will sound and you will get the message:

ERROR - Invalid number. Please try again

BOND SCALE allows you to select a bond, and specify its length in screen units. When you select BOND SCALE, a scale bar is drawn at the left-hand side of the drawing area, and the length of each bond is displayed in green at the centre of the bond. The size of a screen unit is dependent on the size of the screen that you are using. For example, the normal drawing area on a Tek 4207 terminal is 3000 screen units wide and 2460 screen units high. The terminal screen is normally approximately 33 cm, therefore 1cm is approximately equal to 170 screen units.

The structure shown in (i) is on the screen. SCALE will be used to tidy up its bonds.

(i)

Select SCALE
(i) appears in the drawing area. You are then prompted:

Select the atom which will remain fixed:
(Select another command to CANCEL this one)

Select the central C atom
The atom you select is marked with a red cross.

Select the atom which will move:
(Select "CANCEL" if you don't want to SCALE a BOND)

Select the C on the far right
The atom you select is marked with a red cross. You are then prompted:

Use cursor to select the required scale value
OR type the value and press <RETURN>

Type 300
The structure becomes as shown in (ii).
(ii)

By repeatedly selecting bonds and correcting their lenghts, you can tidy up a structure. The result after tidying up all the bonds in the structure in this example is shown in (iii).

(iii)

If there is no bond between the atoms the program will sound an alert and warn:

ERROR - There is no bond between those two atoms - Please try again
Select the atom which will remain fixed:
(Select another command to CANCEL this one)

You can use the numeric keypad on Tek 4200 Series terminals to type the required size, instead of using the cursor to select a size, then press <ENTER> instead of <RETURN>. Using the scale bar, you can only select sizes which are multiples of 10, usually. By typing the number, you can select any integer.

If you do try to type the length, and make a mistake, an alert will sound and you will get the message:

ERROR - Invalid number. Please try again

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Volume 2 Chapter 5 Edit Menu BOND TYPES .