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rp02 - RNApuzzle ready
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mmagnus committed May 19, 2017
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2,106 changes: 2,106 additions & 0 deletions rp02/2_0_solution.pdb
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2,082 changes: 0 additions & 2,082 deletions rp02/2_0_solution_3p59_rpr.pdb
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4,292 changes: 2,148 additions & 2,144 deletions rp02/2_bujnicki_1_rpr.pdb
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4,292 changes: 2,148 additions & 2,144 deletions rp02/2_bujnicki_2_rpr.pdb
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4,292 changes: 2,148 additions & 2,144 deletions rp02/2_bujnicki_3_rpr.pdb
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4,261 changes: 2,148 additions & 2,113 deletions rp02/2_chen_1_rpr.pdb
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4,285 changes: 2,148 additions & 2,137 deletions rp02/2_das_1_rpr.pdb
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4,285 changes: 2,148 additions & 2,137 deletions rp02/2_das_2_rpr.pdb
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4,285 changes: 2,148 additions & 2,137 deletions rp02/2_das_3_rpr.pdb
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4,285 changes: 2,148 additions & 2,137 deletions rp02/2_das_4_rpr.pdb
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4,285 changes: 2,148 additions & 2,137 deletions rp02/2_das_5_rpr.pdb
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4,280 changes: 2,148 additions & 2,132 deletions rp02/2_dokholyan_1_rpr.pdb
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2,137 changes: 0 additions & 2,137 deletions rp02/2_major_1_rpr.pdb
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4,286 changes: 2,149 additions & 2,137 deletions rp02/2_santalucia_1_rpr.pdb
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4,268 changes: 2,148 additions & 2,120 deletions rp02/2_wildauer_1_rpr.pdb
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2,142 changes: 2,142 additions & 0 deletions rp02/problem/2_major_1_rpr.pdb
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74 changes: 73 additions & 1 deletion rp02/readme.md
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Original file line number Diff line number Diff line change
@@ -1,4 +1,76 @@
RNA-Puzzle 02
-----------------------------------------------------------------------------

TODO
Crazy manully fixing with PyMOL.

There is a gap in the native, chain G:

> 2_0_solution G:1-10 13-15
CCGGAGGAACCUG

The native vs models:

```
> 2_0_solution A:1-15
CCGGAGGAACUACUG
> 2_0_solution B:1-10
CCGGCAGCCU
> 2_0_solution C:1-15
CCGGAGGAACUACUG
> 2_0_solution D:1-10
CCGGCAGCCU
> 2_0_solution E:1-15
CCGGAGGAACUACUG
> 2_0_solution F:1-10
CCGGCAGCCU
> 2_0_solution G:1-10 13-15
CCGGAGGAACCUG
> 2_0_solution H:1-10
CCGGCAGCCU
> 2_bujnicki_1_rpr A:1-15
CCGGAGGAACUACUG
> 2_bujnicki_1_rpr B:1-10
CCGGCAGCCU
> 2_bujnicki_1_rpr C:1-15
CCGGAGGAACUACUG
> 2_bujnicki_1_rpr D:1-10
CCGGCAGCCU
> 2_bujnicki_1_rpr E:1-15
CCGGAGGAACUACUG
> 2_bujnicki_1_rpr F:1-10
CCGGCAGCCU
> 2_bujnicki_1_rpr G:1-15
CCGGAGGAACUACUG
> 2_bujnicki_1_rpr H:1-10
CCGGCAGCCU
```

I gave up in fixing `problem/2_major_1_rpr.pdb`.

Edits:

for i in `ls *pdb*`; do rna_pdb_tools.py --rpr $i --inplace;done

```
rna_calc_rmsd.py -t 2_0_solution.pdb --target_selection A:1-15+B:1-10+C:1-15+D:1-10+E:1-15+F:1-10+G:1-10+13-15+H:1-10 --model_selection A:1-15+B:1-10+C:1-15+D:1-10+E:1-15+F:1-10+G:1-10+13-15+H:1-10 *.pdb
rmsd_calc_rmsd_to_target
--------------------------------------------------------------------------------
method: all-atom-built-in
# of models: 13
2_0_solution.pdb 0.0 2094
2_bujnicki_1_rpr.pdb 2.66 2094
2_bujnicki_2_rpr.pdb 2.3 2094
2_bujnicki_3_rpr.pdb 2.33 2094
2_chen_1_rpr.pdb 2.82 2094
2_das_1_rpr.pdb 2.5 2094
2_das_2_rpr.pdb 3.04 2094
2_das_3_rpr.pdb 3.03 2094
2_das_4_rpr.pdb 2.83 2094
2_das_5_rpr.pdb 3.46 2094
2_dokholyan_1_rpr.pdb 2.55 2094
2_santalucia_1_rpr.pdb 3.66 2094
2_wildauer_1_rpr.pdb 3.46 2094
# of atoms used: 2094
csv was created! rmsds.csv
```
14 changes: 14 additions & 0 deletions rp02/rmsds.csv
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fn,rmsd_all
2_0_solution.pdb,0.0
2_bujnicki_1_rpr.pdb,2.66
2_bujnicki_2_rpr.pdb,2.3
2_bujnicki_3_rpr.pdb,2.33
2_chen_1_rpr.pdb,2.82
2_das_1_rpr.pdb,2.5
2_das_2_rpr.pdb,3.04
2_das_3_rpr.pdb,3.03
2_das_4_rpr.pdb,2.83
2_das_5_rpr.pdb,3.46
2_dokholyan_1_rpr.pdb,2.55
2_santalucia_1_rpr.pdb,3.66
2_wildauer_1_rpr.pdb,3.46
207 changes: 151 additions & 56 deletions rp02/seqs.txt
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Original file line number Diff line number Diff line change
@@ -1,126 +1,221 @@
> 2_0_solution_3p59_rpr A:46-60
> 2_0_solution A:1-15
CCGGAGGAACUACUG
> 2_0_solution_3p59_rpr C:46-60
> 2_0_solution B:1-10
CCGGCAGCCU
> 2_0_solution C:1-15
CCGGAGGAACUACUG
> 2_0_solution_3p59_rpr B:104-113
> 2_0_solution D:1-10
CCGGCAGCCU
> 2_0_solution_3p59_rpr E:46-60
> 2_0_solution E:1-15
CCGGAGGAACUACUG
> 2_0_solution_3p59_rpr D:104-113
> 2_0_solution F:1-10
CCGGCAGCCU
> 2_0_solution_3p59_rpr G:46-55 58-60
> 2_0_solution G:1-10 13-15
CCGGAGGAACCUG
> 2_0_solution_3p59_rpr F:104-113
CCGGCAGCCU
> 2_0_solution_3p59_rpr H:104-113
> 2_0_solution H:1-10
CCGGCAGCCU

> 2_bujnicki_1_rpr A:1-15
CCGGAGGAACUACUG
> 2_bujnicki_1_rpr B:1-10
CCGGCAGCCU
> 2_bujnicki_1_rpr C:1-15
CCGGAGGAACUACUG
> 2_bujnicki_1_rpr B:104-113
> 2_bujnicki_1_rpr D:1-10
CCGGCAGCCU
> 2_bujnicki_1_rpr E:1-15
CCGGAGGAACUACUG
> 2_bujnicki_1_rpr D:104-113
> 2_bujnicki_1_rpr F:1-10
CCGGCAGCCU
> 2_bujnicki_1_rpr G:1-15
CCGGAGGAACUACUG
> 2_bujnicki_1_rpr F:104-113
CCGGCAGCCU
> 2_bujnicki_1_rpr H:104-113
> 2_bujnicki_1_rpr H:1-10
CCGGCAGCCU

> 2_bujnicki_2_rpr A:1-15
CCGGAGGAACUACUG
> 2_bujnicki_2_rpr B:1-10
CCGGCAGCCU
> 2_bujnicki_2_rpr C:1-15
CCGGAGGAACUACUG
> 2_bujnicki_2_rpr B:104-113
> 2_bujnicki_2_rpr D:1-10
CCGGCAGCCU
> 2_bujnicki_2_rpr E:1-15
CCGGAGGAACUACUG
> 2_bujnicki_2_rpr D:104-113
> 2_bujnicki_2_rpr F:1-10
CCGGCAGCCU
> 2_bujnicki_2_rpr G:1-15
CCGGAGGAACUACUG
> 2_bujnicki_2_rpr F:104-113
CCGGCAGCCU
> 2_bujnicki_2_rpr H:104-113
> 2_bujnicki_2_rpr H:1-10
CCGGCAGCCU

> 2_bujnicki_3_rpr A:1-15
CCGGAGGAACUACUG
> 2_bujnicki_3_rpr B:1-10
CCGGCAGCCU
> 2_bujnicki_3_rpr C:1-15
CCGGAGGAACUACUG
> 2_bujnicki_3_rpr B:104-113
> 2_bujnicki_3_rpr D:1-10
CCGGCAGCCU
> 2_bujnicki_3_rpr E:1-15
CCGGAGGAACUACUG
> 2_bujnicki_3_rpr D:104-113
> 2_bujnicki_3_rpr F:1-10
CCGGCAGCCU
> 2_bujnicki_3_rpr G:1-15
CCGGAGGAACUACUG
> 2_bujnicki_3_rpr F:104-113
CCGGCAGCCU
> 2_bujnicki_3_rpr H:104-113
> 2_bujnicki_3_rpr H:1-10
CCGGCAGCCU

> 2_chen_1_rpr A:1-100
CCGGCAGCCUCCGGCAGCCUCCGGCAGCCUCCGGCAGCCUCCGGAGGAACUACUGCCGGAGGAACUACUGCCGGAGGAACUACUGCCGGAGGAACUACUG
> 2_chen_1_rpr A:1-15
CCGGAGGAACUACUG
> 2_chen_1_rpr B:1-10
CCGGCAGCCU
> 2_chen_1_rpr C:1-15
CCGGAGGAACUACUG
> 2_chen_1_rpr D:1-10
CCGGCAGCCU
> 2_chen_1_rpr E:1-15
CCGGAGGAACUACUG
> 2_chen_1_rpr F:1-10
CCGGCAGCCU
> 2_chen_1_rpr G:1-15
CCGGAGGAACUACUG
> 2_chen_1_rpr H:1-10
CCGGCAGCCU

> 2_das_1_rpr A:1-100
CCGGCAGCCUCCGGCAGCCUCCGGCAGCCUCCGGCAGCCUCCGGAGGAACUACUGCCGGAGGAACUACUGCCGGAGGAACUACUGCCGGAGGAACUACUG
> 2_das_1_rpr A:1-15
CCGGAGGAACUACUG
> 2_das_1_rpr B:1-10
CCGGCAGCCU
> 2_das_1_rpr C:1-15
CCGGAGGAACUACUG
> 2_das_1_rpr D:1-10
CCGGCAGCCU
> 2_das_1_rpr E:1-15
CCGGAGGAACUACUG
> 2_das_1_rpr F:1-10
CCGGCAGCCU
> 2_das_1_rpr G:1-15
CCGGAGGAACUACUG
> 2_das_1_rpr H:1-10
CCGGCAGCCU

> 2_das_2_rpr A:1-100
CCGGCAGCCUCCGGCAGCCUCCGGCAGCCUCCGGCAGCCUCCGGAGGAACUACUGCCGGAGGAACUACUGCCGGAGGAACUACUGCCGGAGGAACUACUG
> 2_das_2_rpr A:1-15
CCGGAGGAACUACUG
> 2_das_2_rpr B:1-10
CCGGCAGCCU
> 2_das_2_rpr C:1-15
CCGGAGGAACUACUG
> 2_das_2_rpr D:1-10
CCGGCAGCCU
> 2_das_2_rpr E:1-15
CCGGAGGAACUACUG
> 2_das_2_rpr F:1-10
CCGGCAGCCU
> 2_das_2_rpr G:1-15
CCGGAGGAACUACUG
> 2_das_2_rpr H:1-10
CCGGCAGCCU

> 2_das_3_rpr A:1-100
CCGGCAGCCUCCGGCAGCCUCCGGCAGCCUCCGGCAGCCUCCGGAGGAACUACUGCCGGAGGAACUACUGCCGGAGGAACUACUGCCGGAGGAACUACUG
> 2_das_3_rpr A:1-15
CCGGAGGAACUACUG
> 2_das_3_rpr B:1-10
CCGGCAGCCU
> 2_das_3_rpr C:1-15
CCGGAGGAACUACUG
> 2_das_3_rpr D:1-10
CCGGCAGCCU
> 2_das_3_rpr E:1-15
CCGGAGGAACUACUG
> 2_das_3_rpr F:1-10
CCGGCAGCCU
> 2_das_3_rpr G:1-15
CCGGAGGAACUACUG
> 2_das_3_rpr H:1-10
CCGGCAGCCU

> 2_das_4_rpr A:1-100
CCGGCAGCCUCCGGCAGCCUCCGGCAGCCUCCGGCAGCCUCCGGAGGAACUACUGCCGGAGGAACUACUGCCGGAGGAACUACUGCCGGAGGAACUACUG
> 2_das_4_rpr A:1-15
CCGGAGGAACUACUG
> 2_das_4_rpr B:1-10
CCGGCAGCCU
> 2_das_4_rpr C:1-15
CCGGAGGAACUACUG
> 2_das_4_rpr D:1-10
CCGGCAGCCU
> 2_das_4_rpr E:1-15
CCGGAGGAACUACUG
> 2_das_4_rpr F:1-10
CCGGCAGCCU
> 2_das_4_rpr G:1-15
CCGGAGGAACUACUG
> 2_das_4_rpr H:1-10
CCGGCAGCCU

> 2_das_5_rpr A:1-100
CCGGCAGCCUCCGGCAGCCUCCGGCAGCCUCCGGCAGCCUCCGGAGGAACUACUGCCGGAGGAACUACUGCCGGAGGAACUACUGCCGGAGGAACUACUG
> 2_das_5_rpr A:1-15
CCGGAGGAACUACUG
> 2_das_5_rpr B:1-10
CCGGCAGCCU
> 2_das_5_rpr C:1-15
CCGGAGGAACUACUG
> 2_das_5_rpr D:1-10
CCGGCAGCCU
> 2_das_5_rpr E:1-15
CCGGAGGAACUACUG
> 2_das_5_rpr F:1-10
CCGGCAGCCU
> 2_das_5_rpr G:1-15
CCGGAGGAACUACUG
> 2_das_5_rpr H:1-10
CCGGCAGCCU

> 2_dokholyan_1_rpr A:16-30
> 2_dokholyan_1_rpr A:1-15
CCGGAGGAACUACUG
> 2_dokholyan_1_rpr C:31-45
> 2_dokholyan_1_rpr B:1-10
CCGGCAGCCU
> 2_dokholyan_1_rpr C:1-15
CCGGAGGAACUACUG
> 2_dokholyan_1_rpr B:104-113
> 2_dokholyan_1_rpr D:1-10
CCGGCAGCCU
> 2_dokholyan_1_rpr E:46-60
> 2_dokholyan_1_rpr E:1-15
CCGGAGGAACUACUG
> 2_dokholyan_1_rpr D:104-113
> 2_dokholyan_1_rpr F:1-10
CCGGCAGCCU
> 2_dokholyan_1_rpr G:1-15
CCGGAGGAACUACUG
> 2_dokholyan_1_rpr F:104-113
> 2_dokholyan_1_rpr H:1-10
CCGGCAGCCU
> 2_dokholyan_1_rpr H:104-113
CCGGCAGCCU

> 2_major_1_rpr A:1-60 67-106
CUGCCGGAGGAACUACUGCCGGAGGAACUACUGCCGGAGGAACUACUGCCGGAGGAACUACCUCCGGCAGCCUCCGGCAGCCUCCGGCAGCCUCCGGCAG

> 2_santalucia_1_rpr X:1-100
CCGGAGGAACUACUGCCGGAGGAACUACUGCCGGAGGAACUACUGCCGGAGGAACUACUGCCGGCAGCCUCCGGCAGCCUCCGGCAGCCUCCGGCAGCCU
> 2_santalucia_1_rpr A:1-15
CCGGAGGAACUACUG
> 2_santalucia_1_rpr B:1-10
CCGGCAGCCU
> 2_santalucia_1_rpr C:1-15
CCGGAGGAACUACUG
> 2_santalucia_1_rpr D:1-10
CCGGCAGCCU
> 2_santalucia_1_rpr E:1-15
CCGGAGGAACUACUG
> 2_santalucia_1_rpr F:1-10
CCGGCAGCCU
> 2_santalucia_1_rpr G:1-15
CCGGAGGAACUACUG
> 2_santalucia_1_rpr H:1-10
CCGGCAGCCU

> 2_wildauer_1_rpr A:46-60
> 2_wildauer_1_rpr A:1-15
CCGGAGGAACUACUG
> 2_wildauer_1_rpr C:31-45
> 2_wildauer_1_rpr B:1-10
CCGGCAGCCU
> 2_wildauer_1_rpr C:1-15
CCGGAGGAACUACUG
> 2_wildauer_1_rpr B:11-20
> 2_wildauer_1_rpr D:1-10
CCGGCAGCCU
> 2_wildauer_1_rpr E:16-30
> 2_wildauer_1_rpr E:1-15
CCGGAGGAACUACUG
> 2_wildauer_1_rpr D:21-30
> 2_wildauer_1_rpr F:1-10
CCGGCAGCCU
> 2_wildauer_1_rpr G:1-15
CCGGAGGAACUACUG
> 2_wildauer_1_rpr F:31-40
CCGGCAGCCU
> 2_wildauer_1_rpr H:1-10
CCGGCAGCCU

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