Can we output helix-junction-helix structure using DSSR

[lvelve0901]

Hi Xiangjun,

I know that when you run x3dna-dssr on a RNA structure. You can output secondary motif like bulge, hairpin, internal loop etc as a pdb file.
But is there any way that we can search and output structures called helix-junction-helix motif. Junction means either internal loop or bulge while helix means helices with 3 bps.

For example, in 1anr.pdb (HIV-1-TAR), when you run DSSR, there are a dssr-iloops.pdb.
That dssr-iloops file only have G21 A22 U23 C24 U25 G26 C39 U40 C41.
My question is is there any way to also output C19 A20 U42 G43 and A27 G28 C37 U38 to make the stem part like 3 bps long? I plan to calculate inter-helical angles for these helix-junction-helix motif across all the pdb structures. If there is no such option in DSSR, I might have to think about it by myself.

Thank you.

Best,
Honglue

[xiangjun]

Try the --loop=with-stems option.

Xiang-Jun