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Internal loops
xiangjun:
Hi Cigdem,
--- Quote ---This is exactly what I needed! Thank you so much for making things so easier.
--- End quote ---
Glad that it helps! Note also that questions/requests like yours are one of the driving forces that push 3DNA/DSSR forward. So thank you for using DSSR and posting your questions on the 3DNA Forum.
--- Quote ---Just one more thing, if it is applicable could you please also add kink-turn information at the end of the summary line? So that if the corresponding internal loop has a kink-turn, it will say "kt" maybe?
--- End quote ---
Yes. If you download the DSSR again, and run it on 1e7k, the corresponding summary lines would now be as below:
List of 2 internal loops
1 asymmetric internal loop: nts=11; [5,2]; linked by [#1,#2]
summary: [2] 5 2 [C.28 C.45 C.34 C.42] 3 2 k-turn:normal
nts=11 CAAUGAGCGAG C.C28,C.A29,C.A30,C.U31,C.G32,C.A33,C.G34,C.C42,C.G43,C.A44,C.G45
nts=5 AAUGA C.A29,C.A30,C.U31,C.G32,C.A33
nts=2 GA C.G43,C.A44
2 asymmetric internal loop: nts=11; [5,2]; linked by [#3,#4]
summary: [2] 5 2 [D.28 D.45 D.34 D.42] 3 2 k-turn:normal
nts=11 CAAUGAGCGAG D.C28,D.A29,D.A30,D.U31,D.G32,D.A33,D.G34,D.C42,D.G43,D.A44,D.G45
nts=5 AAUGA D.A29,D.A30,D.U31,D.G32,D.A33
nts=2 GA D.G43,D.A44
Since the "summary" field is applied to all DSSR-derived loops, in the future it may contain other relevant useful info for non-k-turn loops as well.
Please let me know if you have any idea to fine-tune the formatting etc. I'm planning a new DSSR release (v1.5.8-2016jul09).
Best regards,
Xiang-Jun
PS. Did you know that you can easily parse DSSR output using the --json option? For example,
--- Code: ---x3dna-dssr -i=1e7k.pdb --json | jq .iloops
--- End code ---
The utility program jq is "a lightweight and flexible command-line JSON processor".
cigdem:
Dear Xiang-Jun,
Thank you for your collaboration. It is perfect!
I agree that in the future you may add information about other motifs as well.
No, I didn't know --json option. It will be so helpful. Thank you for letting me know.
Best regards,
Cigdem
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Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.
