Volume 2 Chapter 5 Edit Menu WHOLE

Function

WHOLE allows the editing operations to be applied to the whole structure.

Remarks

The valid editing operations which can be applied to the whole structure are:

CENTRE
SCALE
DELETE
SHIFT
ROTATE
SYMMETRY
TWIN

Examples

Suppose (i) is the starting fragment.

(i)

Select WHOLE
All atoms of the structure, in both residues, become active.
Select SHIFT

Select any active atom
(or select another command to CANCEL SHIFT)

Select O atom

Now select new position for this atom
(or select another command to CANCEL SHIFT)

Select position b
Fragment is now (ii).
(ii)

You will notice that when O moves to its new position the rest of the structure moves with it.

Note that SHIFT is the default option for WHOLE, so when you select an atom in the active whole structure you are prompted to locate its new position.

The operations ROTATE, CENTRE, SCALE, TWIN behave in an analogous fashion to the examples detailed under RESIDUE.

A check is provided for the DELETE operation. Thus:

Select DELETE
```
Are you sure you want to DELETE the WHOLE structure ? [N]
```
This check provides a safeguard against accidental deletion of the whole structure.

A very useful operation, applicable to WHOLE, BOX and individual residues, is the SYMMETRY command.

Ex. 1 Suppose we have constructed the fragment (i) - see below.

(i)

Suppose WHOLE is active.

Select SYMMETRY
In the bottom right-hand corner of the drawing area appears (ii).
(ii)

Select a symmetry operator: i =inversion centre 10 9 8 7 6543 =rotation axes perpendicular to screen plane - - ? =horizontal and vertical mirrors in screen plane

Select i

Select position of symmetry operator:
(either an existing atom or a point in the drawing area)
(Select CANCEL if you don't want to use SYMMETRY)

Select P atom
(ii) vanishes and the fragment is re-drawn as (iii).
(iii)

Ex. 2 Suppose we have constructed the fragment (iv), WHOLE is active and the SYMMETRY operation has been selected.

(iv)

Select -

Select position of symmetry operator:
 (either an existing atom or a point in the drawing area)
(Select CANCEL if you don't want to use SYMMETRY)

Select the Fe atom in the diagram
```
The two OH2 atoms lie very close to the mirror plane.
```
Both atoms are marked with a green cross in turn and, after an alert, you are prompted each time:
```
WARNING - This atom lies close to the mirror plane!
Do you want to move it to the plane? [Y]
```
If you respond 'Yes' for both atoms, the resulting structure is as shown in (v).
If you respond 'No' for both atoms, the resulting structure is as shown in (vi).

Note that SYMMETRY operations can be applied both to skeleton fragments and to fragments such as (i) where hydrogen constraints have been applied. Indeed other constraints eg charge, total coordination number, etc. will be "replicated" in the symmetry- generated part of the structure.

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