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Hi Xiang-jun,
When I used dssr to extract junctions, I found the junctions for some RNAs share the same stem.
For example, for RNA 4wsm, the output is:
1* 3-way junction: nts=10; [0,4,0]; linked by [#100,#101,#101]
60* 4-way junction: nts=17; [3,1,1,4]; linked by [#211,#212,#282,#212]
76* 5-way junction: nts=14; [0,0,1,3,0]; linked by [#332,#333,#335,#333,#334]
I used the latest version (1.9.6) of dssr, and the command as follows:
x3dna-dssr -i=4wsm.cif -auxfile=no --isolated-pair=not-in-loop -idstr=long -o=4wsm.out
Thanks and best wishes,
Jun
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Hi Jun,
A junction loop derived by DSSR may share the same stem when pseudoknots are involved, as emphased in the DSSR paper (https://doi.org/10.1093/nar/gkv716). See for example, Figure 4 for the env22 twister ribozyme, PDB id: 4rge. Generally speaking, this is a unique feature, instead of a bug, of DSSR. Such junctions are noted with a suffix * after the serial number. One can get rid of such loops by specifying the --nested option.
I've a quick look of your reported case on 4wsm, and noticed that there may be a bug in DSSR. The first case (a three way junction) should not be there. The issue is due to stem#101 (with 2 base pairs) which has a highly distorted geometry, and judged as parallel by DSSR. I will look into the issue further, and get back to you soon.
In the meantime, you could take it as a special case, or simply remove junctions with a * suffix.
Thanks for reporting the issue!
Xiang-Jun
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Hi Xiang-jun,
Even with --nested option, some RNAs still share the same helix. They are 3j7r, 5mrc, 5mre, 5mrf, 6ost.
Best,
Jun
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Hi Jun
Please provide more details with the additional PDB entries, as you did for 4wsm. I believe the underlying issue is similar, most likely associated with extreme cases with distorted structures. The more detailed cases you provide, the better I can test/validate the fixes for the next DSSR release.
Best regards,
Xiang-Jun
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Hi Jun,
I've updated DSSR (still labelled v1.9.6-2019sep16). It should have fixed the junction issue (in the first 3-way junction case) you observed in PDB entry 4wsm. See also my note on junctions with pseudoknots.
Please have a try and report back how it goes. In reporting any further issues, please remain to be specific.
Best regards,
Xiang-Jun
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As a follow-up, I've released DSSR v1.9.7-2019oct01 that's fixed the reported issue.
Xiang-Jun
Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids
Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University