annotate

annotate.json

[
{
  "problem": "ambiguity: multiple matching sequential SS", 
  "resolution": [
    [
      79, 
      {
        "51": {
          "residueid": 20
        }, 
        "i+1": {
          "residueid": 21, 
          "aatype": "F"
        }, 
        "type": "inconsistent with sequence, seq-specific assns -- need a Phenylalanine", 
        "79": {
          "residueid": 32, 
          "aatype": "K"
        }
      }, 
      {
        "51": 20, 
        "type": "inconsistent with sequential assignments", 
        "79": 32
      }
    ], 
    [
      110, 
      {
        "CA(i+1)(i)": {
          "amp": 35.05, 
          "peakid": [
            "hncacb", 
            634
          ]
        }, 
        "type": "matching peaks not i-1", 
        "CA(i+1)(i-1)": {
          "amp": 6.438, 
          "peakid": [
            "hncacb", 
            636
          ]
        }, 
        "CA(i)": {
          "amp": 12.93, 
          "peakid": [
            "hncacb", 
            302
          ]
        }
      }
    ], 
    [
      77, 
      {
        "type": "appears to be consistent"
      }
    ]
  ], 
  "spin systems": {
    "i": 51, 
    "i+1": [
      79, 
      110, 
      77
    ]
  }
},

{
  "problem": "ambiguity: multiple matching sequential SS", 
  "resolution": [
    [
      31, 
      {
        "i": {
          "amp": 6.438, 
          "peakid": [
            "hncacb", 
            636
          ]
        }, 
        "other": {
          "amp": 28.53, 
          "peakid": [
            "hncacb", 
            218
          ]
        }, 
        "type": "matching CA peak was an i-1, not an i", 
        "matching": {
          "amp": 7.346, 
          "peakid": [
            "hncacb", 
            220
          ]
        }
      }, 
      {
        "residueids": {
          "i": 31, 
          "potential i-1": 95
        }, 
        "type": "inconsistency of SS-residue assignments"
      }
    ], 
    [
      96, 
      {
        "residueids": {
          "i": 31, 
          "potential i-1": 94
        }, 
        "type": "inconsistency of SS-residue assignments"
      }, 
      {
        "type": "preceding aatype unlikely to be V, as required by the sequence and SS110's assignments, based on BMRB statistics", 
        "side 2": {
          "i-1 peaks": {
            "CB": 42.364, 
            "CA": 56.537
          }
        }, 
        "side 1": {
          "assignment": {
            "residueid": 31, 
            "ssid": 110
          }, 
          "i-2": {
            "residueid": 29, 
            "aatype": "V"
          }, 
          "BMRB statistics": {
            "CB": 32.714, 
            "CA": 62.563
          }
        }
      }
    ], 
    [
      135, 
      {
        "type": "correct i/i-1 peak type and preceding aatype"
      }
    ]
  ], 
  "spin systems": {
    "i": 110, 
    "i-1": [
      31, 
      96, 
      13
    ]
  }
},

  {
    "problem": "ambiguity: multiple matching sequential SS", 
    "resolution": [
      [
        77, 
        {
          "CB": {
            "i": {
              "amp": -14.21, 
              "peakid": [
                "hncacb", 
                489
              ]
            }, 
            "other": {
              "amp": -7.75, 
              "peakid": [
                "hncacb", 
                474
              ]
            }, 
            "matching": {
              "amp": -3.487, 
              "peakid": [
                "hncacb", 
                472
              ]
            }
          }, 
          "CA": {
            "i": {
              "amp": 14.3, 
              "peakid": [
                "hncacb", 
                488
              ]
            }, 
            "other": {
              "amp": 12.56, 
              "peakid": [
                "hncacb", 
                471
              ]
            }, 
            "matching": {
              "amp": 5.17, 
              "peakid": [
                "hncacb", 
                473
              ]
            }
          }, 
          "type": "matching peaks seemed to be i-1 peaks, and not preceded by G (sequence, seq-specific assns)"
        }
      ], 
      [
        51, 
        {
          "type": "not preceded by G"
        }
      ], 
      [
        110, 
        {
          "type": "preceded by G, i peaks match SS79(i-1) peaks"
        }
      ]
    ], 
    "spin systems": {
      "i": 79, 
      "i-1": [
        77, 
        51, 
        110
      ]
    }
  }, 
  {
    "problem": "ambiguity: multiple matching sequential SS", 
    "resolution": [
      [
        76, 
        {
          "type": "missing expected peak: no CB peak to match the i-1 of SS119", 
          "causes": [
            {
              "type": "missing expected CB(i-1) peak", 
              "peakid": [
                "hncacb", 
                673
              ]
            }
          ]
        }
      ], 
      [
        87, 
        {
          "type": "matching CA peak seemed to be an i-1, not an i", 
          "causes": [
            {
              "peakid": [
                "hncacb", 
                669
              ], 
              "type": "CA(i-1) peak", 
              "ssid": 119
            }, 
            {
              "peakid": [
                "hncacb", 
                532
              ], 
              "type": "matching CA peak", 
              "ssid": 87, 
              "amp": 7.36
            }, 
            {
              "peakid": [
                "hncacb", 
                534
              ], 
              "type": "other CA peak", 
              "ssid": 87, 
              "amp": 19.47
            }
          ]
        }
      ], 
      [
        79, 
        {
          "type": "not inconsistent: matches CA, CB peaks"
        }
      ]
    ], 
    "spin systems": {
      "i": 119, 
      "i-1": [
        76, 
        87, 
        79
      ]
    }
  }, 
  {
    "problem": "ambiguity: multiple matching sequential SS", 
    "resolution": [
      [
        135, 
        {
          "type": "inconsistency between sequence, sequence-specific assignments", 
          "causes": [
            {
              "residueid": 95, 
              "type": "ss/res assignment", 
              "ssid": 31
            }, 
            {
              "residueid": 93, 
              "type": "primary sequence", 
              "aatype": "D"
            }, 
            {
              "type": "BMRB statistics", 
              "aatype": "D", 
              "shifts": {
                "CB": 40.876, 
                "CA": 54.705
              }
            }, 
            {
              "shifts": {
                "CB": 32.036, 
                "CA": 64.384
              }, 
              "type": "i-1, HNCACB peaks", 
              "ssid": 135
            }
          ]
        }
      ], 
      [
        132, 
        {
          "type": "missing expected i-1 peaks; suspect it's two consecutive G residues", 
          "causes": [
            {
              "type": "expected peaks -- BMRB statistics", 
              "atomtypes": {
                "CB": 40.876, 
                "CA": 54.705
              }, 
              "aatype": "D"
            }, 
            {
              "atomtypes": {
                "CB": null, 
                "CA": null
              }, 
              "type": "missing peaks -- i-1", 
              "ssid": 132
            }
          ]
        }
      ], 
      [
        50, 
        {
          "type": "inconsistency of CB compared to BMRB statistics", 
          "causes": [
            {
              "residueid": 95, 
              "type": "ss/res assignment", 
              "ssid": 31
            }, 
            {
              "residueid": 93, 
              "type": "primary sequence", 
              "aatype": "D"
            }, 
            {
              "type": "BMRB statistics", 
              "aatype": "D", 
              "peak": "CB", 
              "shifts": {
                "CB": 40.876
              }
            }, 
            {
              "type": "i-1, HNCACB peaks", 
              "peakid": [
                "hncacb", 
                317
              ], 
              "ssid": 135, 
              "shifts": {
                "CB": 32.036
              }
            }
          ]
        }, 
        {
          "type": "SS must be G, therefore CA(i) should be in G range, but peak in G range has smaller intensity than other CA peak", 
          "causes": [
            {
              "type": "CA(i-1)", 
              "c": 45.198, 
              "peakid": [
                "hncacb", 
                220
              ], 
              "ssid": 31
            }, 
            {
              "type": "CA of SS50", 
              "c": 45.238, 
              "peakid": [
                "hncacb", 
                313
              ], 
              "amp": 53.87
            }, 
            {
              "type": "CA of SS50", 
              "c": 56.063, 
              "peakid": [
                "hncacb", 
                310
              ], 
              "amp": 56.01
            }
          ]
        }
      ]
    ], 
    "spin systems": {
      "i": 31, 
      "i-1": [
        50, 
        96, 
        132, 
        135
      ]
    }
  }
]