NMRFAM-Sparky: Semi-Automated peak assignments

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This page gives instruction on the semi-automated peak assignment functions of NMRFAM-Sparky

  1. Open HSQC in NMRFAM-Sparky
  2. Navigate to NMRFAM -> Superfast side chain assignment -> dummy graph
  3. Open the .seq or .fasta file for the protein
    1. This will open a graph of all amino acid residues in sequence
  4. Navigate to NMRFAM -> Superfast side chain assignment -> Transfer and simulate assignments
    1. Choose type of spectra (ie N-HSQC)
    2. Enter BMRB ID and click simulate
    3. This marks "peaks" at each coordinate for each residue from BMRB file
  5. Manually center marker on peak and untag residue
    1. Move the crosshair to the corresponding peak and center using command "cu"
    2. H and N for this residue in dummy graph should have black circle around it meaning peak is assigned
  6. "lt" gives a peak list that shows untagged residues which will be used later
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