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Topics - jyesselm

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RNA structures (DSSR) / DSSR issue --json and --analyze
« on: April 19, 2020, 11:20:27 pm »
Hi Xiang-Jun,

I must again commend you on your amazing software. Not only is it quite useful but you are incredibly responsive to issues.

I have downloaded your new version of DSSR and love the json support. I noticed though that if I use both --json and --analyze it will suppress the json output. It would be amazing if you can add in the --analyze info into the json.

x3dna-dssr -i=S_000001.pdb --json --analyze

Best,
Joe

2
General discussions (Q&As) / base pair frame from base frames
« on: February 26, 2014, 06:40:53 pm »
Hi Xiang-Jun,

I was hoping you could help me understand part of your tech_details.pdf. I was able to follow up to calculating the reference frame of each base and I am trying to understand how you combine them into "middle frame", presumably this is base pair frame? Shown on page 6 for base pair A_G1-B_C8.

Thank you very much.
-Joe

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Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.