Pre Assignment Instruction

  
 
  • PINE can carry out assignments on proteins that have been previously partially assigned either manually or by other automated software.
  • This is accomplished by including a “pre-assignment file” as input to PINE.
  • To yield the best results, include only the assignments of residues that you are 100% sure of in the pre-assignment file. Pine will not change the assignment for any residue with a pre-assignment. It will also use the pre-assignment in assigning other residues.
  • Upload the protein sequence file and all available peak list files along with the pre-assignment file in the PINE webserver.
  • The pre-assignment file should be reported in BMRB format, see the sample below (Again, include only the residues with assignments known to be 100% correct.) The Header and Footer are not required. Only the highlighted part is required.  
  • The easiest way to generate pre-assignment file is typing two-letter code "ep" in the NMRFAM SPARKY distribution.  
 		  
 

 

Example of a Pre-Assignment File

 

  
  loop_

_Atom_shift_assign_ID

_Residue_seq_code

_Residue_label

_Atom_name

_Atom_type

_Chem_shift_value

_Chem_shift_value_error

_Chem_shift_ambiguity_code

 

 1   15  ARG    C     C  175.707  1.000  0

  2   15  ARG   CA     C   55.844  1.000  0

  3   15  ARG   CB     C   30.781  1.000  0

  4   16  VAL    N     N  123.241  1.000  0

  5   16  VAL    H     H    8.160  1.000  0

  6   16  VAL    C     C  176.086  1.000  0

  7   16  VAL   CA     C   62.219  1.000  0

  8   16  VAL   CB     C   32.444  1.000  0

  9   17  MET    N     N  125.650  1.000  0

  10   17  MET    H     H    8.417  1.000  0

  11   17  MET    C     C  176.449  1.000  0

  12   17  MET   CA     C   54.894  1.000  0

  13   17  MET   CB     C   32.483  1.000  0

  14   18  GLY    N     N  110.622  1.000  0

  15   18  GLY    H     H    8.256  1.000  0

  16   18  GLY    C     C  173.934  1.000  0

  17   18  GLY   CA     C   44.877  1.000  0

  18   25  LYS    C     C  176.523  1.000  0

  19   25  LYS   CA     C   56.042  1.000  0

  20   25  LYS   CB     C   33.065  1.000  0

  21   26  GLY    N     N  110.854  1.000  0

  22   26  GLY    H     H    8.168  1.000  0

  23   26  GLY   CA     C   44.181  1.000  0

 

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