Messages

1

Bug reports / Re: When analyzing multiple frames with --nmr, DSSR gets slower with each frame

« on: June 13, 2025, 09:58:08 am »

I see.  That makes sense where the slowdown is coming from.  For what its worth, in tools I've worked on in the past, when we need to do random-access trajectory reading, we first read through the whole trajectory once and make an index of the byte offsets for the start of each frame.  That way you can jump to any arbitrary frame without having to search through the file each time.

2

RNA structures (DSSR) / Re: Using --helical-axis with the --nmr option in DSSR

« on: June 13, 2025, 08:52:05 am »

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

3

Bug reports / When analyzing multiple frames with --nmr, DSSR gets slower with each frame

« on: June 12, 2025, 08:48:31 am »

When I analyze MD trajectories with the --nmr option, the runtime does not scale linearly with the number of frames as one might expect.  For the same structure here are some benchmarks:

n_frames	runtime (hh:mm)
2500	1:00
5000	4:15
10000	>15:00

This suggests to me that there is either some sort of memory leak or maybe the file writing is seeking to the end of the file at the end of each frame?

Here is my DSSR command:

Code: [Select]

~/software/x3dna-dssr -i=RNA_traj.pdb --nmr --json -o=dssr.json
DSSR version: 2.4.6-2024nov15

4

RNA structures (DSSR) / Using --helical-axis with the --nmr option in DSSR

« 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?