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Messages - sankaran

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RNA structures (DSSR) / Query in 3DNA-DSSR output vs W3DNA output
« on: February 27, 2021, 10:53:38 pm »
I am a Postgraduate student currently pursuing a project. For my project work, I am using 3DNA-DSSR (v1.9.10-2020apr23.) to calculate the DNA shape parameters. I am writing to you to get clarity on the output from the x3DNA-DSSR and the W3DNA. The base step parameters from the 3DNA-DSSR and W3DNA are different. In the DSSR, the step parameters (Shift, Slide, Rise, Tilt, Roll, Twist) for the last base pair is given as 9999 whereas, in the output from the web server, the step parameters for the first base pair is given as 0.000. Considering the fact that the base pair step parameters are calculated based on the current and previous base pairs, 0.00 for the first base pasir would be ideal. but in the case of DSSR, the first base pair gets the value. Can you please let me know why is there a difference? I have attached the output files along with the PDB.
Thank you

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