High evidence interactions not included in hybrid-ss-min fold

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JP
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Joined: 08/28/2019

Hello,

I am hoping you can give some insight into an issue I am experiencing with hybrid-ss-min. When I run hybrid-ss-min with just 1 contsraint, e.g:

F 3998 5059 5

This constraint is not included in the folded result. It seems when I choose any constraint more than 300bp apart it is not included. I have manually checked the base pairing of these nucleotides, and manually set the --maxbp option. Have you ever noticed this behaviour before?

Any help / advice would be greatly appreciated.

Many thanks,

Jon

JP
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Joined: 08/28/2019
positive energy structure

Will hybrid-ss-min ever output a structure with positive free energy?