Using --helical-axis with the --nmr option in DSSR

[rkpoppleton]

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?

[xiangjun]

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

[rkpoppleton]

Thank you!  The --more option was what I was missing.