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Visualizing secondary RNA structure binding to target

I am designing synthetic ribozymes, and need to see the secondary structure that arises from its flanking arms binding to a target mRNA. I've used Mfold as well as IDT's OligoAnalyzer (Hairpin), but ...
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How to model missing residues on a protein from multiple PDB files?

I have multiple X-ray structures (PDB files) of the same protein. All of them have missing stretches of residues. I want to use all of them to build a single model, with as little missing residues as ...