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Questions and answers > RNA structures (DSSR)

can i get the cross_chain base-pair as a dot-bracket notation just use dssr

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langmei:
hi,
 I want to get the interaction base pair across the chain, but the dssr default output is the  base-pair of the whole the sequence ,can i use a optation to get the cross-chain interaction of two chain?
 thanks!

xiangjun:
I get what you're saying, but I'm having trouble imagining how the requested new feature would be used. Please give specific examples to demonstrate what you're trying to accomplish.

Best regards,

Xiang-Jun

langmei:
I will use the new feature to predict the base level interaction of two chain, so i need to obtain the cross chain base_pair notation (not include the inter chain inter chain base interaction)

xiangjun:
Only two chains? How about more than two chains? What do you mean by "the cross chain base_pair notation"?

langmei:
all the chain interaction in one pdb file, i want to get the dot-bracket of cross chain interaction. thank you!

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Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.