Volume 2 Chapter 1 Build menu FUSE

Function

FUSE is used to join together two fragments, with the deletion of two atoms and one bond.

Examples

Ex. 1 Suppose the drawing area contains (i) - see below.

Select FUSE

Two residues will be FUSEd together.
Select TWO ATOMS from FIRST residue

Select atom a
Select atom b
We now have red + at atoms a and b.

Now select TWO ATOMS from SECOND residue

Select atom p
Select atom q
We now have red + at atoms p and q.
Screen clears and fragment is re-drawn as (ii).

Ex. 2 Suppose the drawing area contains (i).

Select FUSE

Two residues will be FUSEd together.
Select TWO ATOMS from FIRST residue

Select atom a
Select atom b
We now have red + at atoms a and b

Now select TWO ATOMS from SECOND residue

Select atom q
Select atom p
We now have red + at atoms q and p.
Screen clears and fragment is re-drawn as (iii).

The above two examples illustrate how important it is to specify the atoms in the correct order. You should note that when the fused system is drawn then the position of residue 1 is not changed from its position prior to the FUSE operation, unless the resultant structure would not fit on the screen.

You should also note that normally the "fusion bond" in residue 1 determines the element type and bond type of the "fusion bond" after fusion has taken place. However, there is one situation where this is over-ridden - if the bond type of the second bond is aromatic. In this case the resultant bond will always be aromatic, and the following message will be issued after an alert:

Note - The fused bond type will be aromatic!
Please press <RETURN> to continue. Thank you.

Ex. 3 Suppose the drawing area contains (i) - see below.

Select FUSE

Two residues will be FUSEd together.
Select TWO ATOMS from FIRST residue

Select atom a
Select atom b
We now have red + at atoms a and b.

Now select TWO ATOMS from SECOND residue

Select atom p
Select atom q
We now have red + at atoms p and q
Screen clears and fragment is re-drawn as (ii).

Ex. 4 Although we normally regard fusion to involve the fusion of rings in fact the FUSE option can be generalised to the fusion of two bonds in non-ring residues.

Suppose the drawing area contains (iii).

Select FUSE

Two residues will be FUSEd together.
Select TWO ATOMS from FIRST residue

Select atom a
Select atom b
We now have red + at atoms a and b.

Now select TWO ATOMS from SECOND residue

Select atom c
Select atom d
We now have red + at atoms c and d.
Screen clears and fragment is re-drawn as (iv).

You should note the following three error situations:

(a)

Suppose the drawing area contains:

Select FUSE

Two residues will be FUSEd together.
Select TWO ATOMS from FIRST residue

Select atom a
Select atom b

These are in different RESIDUES. Please reselect:
Select TWO ATOMS from FIRST residue

(b)

Suppose the drawing area contains:

Select FUSE

Two or more residues are required for FUSE

(c)

When you are prompted to select two atoms from a residue then the program expects that these atoms will be bonded to each other. If not, the resulting fused system may be disastrous! However, you can use UNDO to reverse the operation.

Note: In the FUSE operation any resultant overlapping atoms are eliminated.

For example, fuse:

then an atom is eliminated.

The easiest way to check for overlapping atoms is to select NUMBERS in the 2D-CONSTRAIN sub- menu.

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Volume 2 Chapter 1 Build menu GRID .