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General discussions (Q&As) / Dimer Analysis Using find_pair
« on: February 08, 2017, 12:01:42 am »
Hello,
I’ve been having some issues running ‘find_pair’ in 3DNA. I have a strand of DNA that contains two thymine dimers. The issue is it is able to find the pairs for one of the dimers but not the other. The other issue is that it does not detect the base pairs at the end of the DNA strand.
I’m wondering how ‘find_pair’ analyzes these dimers?
I’m also wondering how to modify the output file of ‘find_pair’ to include these bases that it is missing?
I have attached the .pdb file I am trying to run ‘find_pair’ on.
Thank you
I’ve been having some issues running ‘find_pair’ in 3DNA. I have a strand of DNA that contains two thymine dimers. The issue is it is able to find the pairs for one of the dimers but not the other. The other issue is that it does not detect the base pairs at the end of the DNA strand.
I’m wondering how ‘find_pair’ analyzes these dimers?
I’m also wondering how to modify the output file of ‘find_pair’ to include these bases that it is missing?
I have attached the .pdb file I am trying to run ‘find_pair’ on.
Thank you