Hi all,
I am using the newest DSSR to extract the junction structure, but the stems of some junctions have only one base pair. Take 5vyc.cif for an example and one of its 3-way junctions is as follows:
1 3-way junction: nts=11; [2,1,2]; linked by [#63,#64,#-49]
summary: [3] 2 1 2 [i2.1225 i2.1641 i2.1228 i2.1530 i2.1532 i2.1638] 5 3 1
nts=11 UGGAUACGGAA 1..i2.U.1225.,1..i2.G.1226.,1..i2.G.1227.,1..i2.A.1228.,1..i2.U.1530.,1..i2.A.1531.,1..i2.C.1532.,1..i2.G.1638.,1..i2.G.1639.,1..i2.A.1640.,1..i2.A.1641.
nts=2 GG 1..i2.G.1226.,1..i2.G.1227.
nts=1 A 1..i2.A.1531.
nts=2 GA 1..i2.G.1639.,1..i2.A.1640.
The last stem #-49 has only one base pair. There are many cases like this in the output. Is it reasonable to take structure like this as a junction?
Thanks,
Jun Li