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Hello,
I have a RNA duplex with a bulge on one strand. I want to calculate the helicoidal parameters by excluding the bulge part. When i run the find_pair followed by analyze, it takes the whole structure and analyze. To be precise, is there any way that i can do the analysis only on a specific portion of my interest.
It would be highly helpful if someone could wite me your experience (some ref's) on using 3DNA for irregular nuc. acid structure.
regards,
Bala
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"find_pair" generates an input file in text format that you can edit to suit your specific need before feeding into "analyze" (or "cehs").
Just imagine the situation without access to "find_pair": how would you prepare (from a nucleic acid containing structure in PDB format) an input file for an analysis program such as Curves etc?
In the 3DNA homepage, I have also maintained a list of citations to 3DNA (http://http://rutchem.rutgers.edu/~xiangjun/3DNA/citations.html) compiled from Web of Science. It is not necessarily complete, but could serve as a good starting point to related published work.
So far, I've been the only person in answering questions in the forum. That's fine as a starting point. In the long run, I do hope other colleagues would get more actively involved: not only in asking questions, but also in answering them; moreover, in sharing your experiences, or contributing scripts/programs etc. Your contribution can make a difference (http://http://rutchem.rutgers.edu/~xiangjun/3DNA/users.html)!
HTH,
Xiang-Jun