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RNA structures (DSSR) / Avoiding pairing that cross chains

« on: July 26, 2019, 01:11:05 pm »

I used DSSR to calculate the secondary structure of PDB 4V6W chain A5, which is a eukaryotic LSU rRNA. This resulted in 896 left pairings "(" and 880 right pairings ")". Presumably this imbalance is because some of the pairs are inter-chain. Is there a way to force pairings only within single chains (i.e., intra-chain pairs only)? Ideally, I would like to obtain a balanced structure for each chain by itself.

Thanks,
Erik