3DNA Forum

Questions and answers => RNA structures (DSSR) => Topic started by: rkpoppleton on June 12, 2025, 08:27:14 am

Title: Using --helical-axis with the --nmr option in DSSR
Post by: rkpoppleton on June 12, 2025, 08:27:14 am: Hi! Thanks for the excellent tool, DSSR has solved so many problems in my analysis of RNA MD simulations! I am currently trying to calculate the angle between two helices in an RNA structure. For any single configuration, I can use the --helical-axis option to get the helical axes as a .pdb file, which works very well. However this file seems to be overwritten for every frame if you run DSSR on multiple frames with the --nmr option. I looked around in the --json output, but I can't seem to find a per-model output there.

Are the helix axes output anywhere and I just missed them, or is there something else I need to do to get the dssr-helicalAxes.pdb file on a per-model basis?
Title: Re: Using --helical-axis with the --nmr option in DSSR
Post by: xiangjun on June 12, 2025, 02:57:39 pm: Hi,

Thanks for your kind words about DSSR. Please try the --more option which will output "helical-axis", "point-one" and "point-one" as documented in the DSSR User Manual. You could parse the corresponding output for each model and start from there to calculate the bending angle.

Hope this helps.

Xiang-Jun
Title: Re: Using --helical-axis with the --nmr option in DSSR
Post by: rkpoppleton on June 13, 2025, 08:52:05 am: Thank you! The --more option was what I was missing.