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Questions and answers => RNA structures (DSSR) => DSSR-Jmol integration => Topic started by: xiangjun on May 04, 2017, 01:45:06 pm

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Title: Table 1
Post by: xiangjun on May 04, 2017, 01:45:06 pm
Here is Table 1 and the corresponding DSSR/jq (https://stedolan.github.io/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
  1. Accessible features (16 keys)  ["pairs","multiplets","helices","stems","isoCanonPairs","coaxStacks","hairpins","bulges","iloops","junctions","kissingLoops","ssSegments","stacks","nonStack","hbonds","nts"]
  2.                                // x3dna-dssr --json=ebi -i=1ehz.cif | jq -c '.paths | keys_unsorted'
  3.  
  4. 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}
  5.                                // x3dna-dssr --json=ebi -i=1ehz.cif | jq -c .counts
  6.                                
  7. 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"}
  8.                                // x3dna-dssr --json=ebi -i=1ehz.cif | jq -c .pairs[0]
  9.                                
  10. Nucleotide (2MG10)             {"nt_name":"2MG","nt_id":"|1|A|2MG|10||||","is_modified":true,"chi":169.599,"puckering":"C3'-endo"}
  11.                                // x3dna-dssr --json=ebi -i=1ehz.cif | jq -c '.nts[9] | {nt_name, nt_id, is_modified, chi, puckering}'
  12.  
  13. Jmol (SQL) selections          SELECT hairpins
  14.                                SELECT within(dssr, "nts WHERE is_modified")
  15.                                SELECT within(dssr, "pairs WHERE name !='WC'")
  16.  

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.