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Questions and answers => General discussions (Q&As) => Topic started by: emilita96 on February 08, 2017, 12:01:42 am

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Title: Dimer Analysis Using find_pair
Post by: emilita96 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
Title: Re: Dimer Analysis Using find_pair
Post by: xiangjun on February 08, 2017, 12:13:11 am
Hi,

Your attached test.pdb is a nucleosomal DNA, with distorted regions. Thus it is not surprising that 3DNA may not find base pairs as 'expected'. See FAQ entry "How to fix missing (superfluous) base pairs identified by find_pair? (http://forum.x3dna.org/faqs/how-to-fix-missing-(superfluous)-base-pairs-identified-by-find_pair/)" on how to manually edit the output from find_pair before feeding it into the 3DNA analyze program.

See the two 3DNA papers (2003 NAR, and 2008 Nature Protocols) on how base pairs are identified. Both PDFs are included in the doc/ directory with 3DNA v2.3 distribution.

HTH,

Xiang-Jun

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.