Recent Posts

81

RNA structures (DSSR) / Re: Building G-quadruplexes

« Last post by shr on June 20, 2025, 02:38:28 am »

It looks like this can definitely be used as a building block. Is the DSSR code for G-Quadruplex open-source? If I may ask, would it be possible to look into the code? In my code, I tried to add more stacks but it seems a little tricky to do considering the backbone also needs to be bonded together.

With regards
Shreyasi Das

82

DNA/RNA-protein interactions (SNAP) / Re: Implement Json

« Last post by xiangjun on June 13, 2025, 04:19:01 pm »

Hi,

Thanks for using SNAP/DSSR and for posting your question on the Forum.

The --json option is available in the DSSR Pro version (x3dna-dssr snap --json) . This is one of the few features that is currently not enabled in the free DSSR Basic Academic version. No paper on SNAP has been published yet. Some features need further developments and better documentation. I may consider enable more Pro features in the Basic version in the future.

The general principle of 3DNA/DSSR is to ensure that published results and documented features (in the DSSR Manual) are reproducible. DSSR has more to offer than those published/documented.

Best regards,

Xiang-Jun

83

DNA/RNA-protein interactions (SNAP) / Re: Implement Json

« Last post by kyle_ on June 13, 2025, 04:02:02 pm »

Hello,
I am using SNAP via `x3dna-dssr snap -i=my_file.pdb` and have found the output very useful, but am hoping to export it as JSON to automate some of my analysis. I see how I can run `x3dna-dssr -i=my_file.pdb --json`, and it seems that when `x3dna-snap` was packaged separately it had also a `--json` flag for this purpose (eg. https://x3dna.org/articles/h-bonds-reported-by-dssr-and-snap). Such a flag no longer seems to work with `x3dna-dssr snap -i=my_file.pdb --json`, so I am asking: does this JSON format functionality still exist for SNAP output? Perhaps it exists and this flag is not the way to access it.

84

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

« Last post by xiangjun on June 13, 2025, 10:36:42 am »

It sounds like a good suggestion. I will think about it.

85

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

« Last post by rkpoppleton 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.

86

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

« Last post by rkpoppleton on June 13, 2025, 08:52:05 am »

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

87

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

« Last 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

88

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

« Last post by xiangjun on June 12, 2025, 02:51:55 pm »

Hi,

Thanks for using DSSR and for posting your question on the Forum. I am aware of the issue you are describing. The initial design of the --nmr option allows for flexibility of user-selected frames/models (e.g., --nmr=3+5+6:9 as described in the User Manual). For each frame/model, DSSR re-reads the input file from the beginning, which causes the slowdown as you observed. There is no memory leak, as you can verify with valgrind or similar tools.

DSSR Pro version allows for sequential processing of all the frames in a single pass, which leads to faster performance (scale linearly with the number of frames).

Best regards,

Xiang-Jun

89

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

« Last post by rkpoppleton 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

90

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

« Last 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?