DNA bend angle

[narayana]

Dear Dr. Lu,

Is there a way to compute bending angle using DSSR program. From your manual I do note that it is possible, but I am not sure how I can specify to do this. For example, for 1fjl, what would be the command line instructions? Your suggestion is much appreciated.

Thank you.

Narendra

[xiangjun]

Hi Narendra,

Thanks for using DSSR and for posting your question on the 3DNA Forum. Regarding DNA bending angle in 3DNA/DSSR, please refer to the FAQ How to calculate DNA bending angle?. With DSSR, the helical axis info is available with the --more option. See the step-by-step procedures for reproducing Figure 2 -- analysis of the yeast phenylalanine tRNA (1ehz) of the 2015 DSSR paper in NAR.

For your specific example of 1fjl, DSSR readily identifies a helix (stem) with details on the helical axis. However, DSSR does not directly provide you a bending angle for reason given in the above mentioned FAQ.

Best regards,

Xiang-Jun