This command also describes a CTransfoFG and is used to define the relations that will be used to place residues not adjacent in the sequence. Typically, the relation will involve hydrogen bond between the bases. Base pairings are described using the operator '/' which takes two operands, the former applying to the first residue in the statement and the latter applying to the second.
pair (<pairDescription>+)
| <pairDescription> | = | <residueId1> <residueId2> <properties> <set size> |
An example would be:
Example:
pair
(
A12 A26 { W / H pairing cis } 10
)
|
where this means that we are looking for pairings involving the Watson-Crick edge of A12 and the Hoogsteen egde of A26. Some other examples:
Example:
pair
(
A11 A26 { wct } 100%
A12 A25 { wct } 100%
A13 A24 { wct } 100%
A14 A23 { wct } 1
A15 A22 { wct } 1
A16 A21 { cis && W / W } 1
A17 A20 { trans && S / H } 25
A1 A6 { Ww / Ww && strong } 5
A2 A5 { Ww / any && strong } 5 // any means any faces for A5
A3 A4 { Hh / (Ww || Hh) && strong } 3
B1 B9 { (Ww / Ww && cis) || (Ww / H && trans) } 3
)
|