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Questions and answers > DSSR-Jmol integration
Table 1
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xiangjun:
Here is Table 1 and the corresponding DSSR/jq command for each example item on the right column [other than "Jmol (SQL) selections"].
Table 1. DSSR-derived features and DSSR-specific selections in Jmol, using yeast phenylalanine tRNA (1ehz) as an example
--- Code: Javascript ---Accessible features (16 keys) ["pairs","multiplets","helices","stems","isoCanonPairs","coaxStacks","hairpins","bulges","iloops","junctions","kissingLoops","ssSegments","stacks","nonStack","hbonds","nts"] // x3dna-dssr --json=ebi -i=1ehz.cif | jq -c '.paths | keys_unsorted' Actual counts (1ehz) {"pairs":34,"multiplets":4,"helices":2,"stems":4,"isoCanonPairs":1,"coaxStacks":2,"hairpins":3,"junctions":1,"kissingLoops":1,"ssSegments":1,"stacks":11,"nonStack":4,"hbonds":118,"nts":76} // x3dna-dssr --json=ebi -i=1ehz.cif | jq -c .counts Base pair (G1–C72) {"index":1,"nt1":"|1|A|G|1||||","nt2":"|1|A|C|72||||","bp":"G-C","name":"WC","Saenger":"19-XIX","LW":"cWW","DSSR":"cW-W"} // x3dna-dssr --json=ebi -i=1ehz.cif | jq -c .pairs[0] Nucleotide (2MG10) {"nt_name":"2MG","nt_id":"|1|A|2MG|10||||","is_modified":true,"chi":169.599,"puckering":"C3'-endo"} // x3dna-dssr --json=ebi -i=1ehz.cif | jq -c '.nts[9] | {nt_name, nt_id, is_modified, chi, puckering}' Jmol (SQL) selections SELECT hairpins SELECT within(dssr, "nts WHERE is_modified") SELECT within(dssr, "pairs WHERE name !='WC'")
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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.