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Topics - Shuming_Liu

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Hi everyone,

These days I am trying to build a model by concatenating two DNA chains together. I followed this tutorial: http://forum.x3dna.org/users-contributions/build-dna-bulges-and-extend-dna-duplex-at-both-terminals-via-3dna/

I have used find_pair and frame_mol to align the ends of two DNA chains. However, I have met the problem that I cannot control the direction in which they are concatenated. That is to say, I imagine after concatenating them together by overlapping the ending base pairs, both chains will extend in different directions; but the result is that the two chains are extending in the same direction and largely overlaps. I don't know how to control the direction in which the endings of two chains are aligned. I have tried to change chain ID as well as change residue ID, but they also do not work. So I am wondering if someone has experience in solving such problems, thanks!

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Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.