InSane: resonance assignments



The shifts command in the NMR menu may be used to read in resonance assignments: e.g.
NMR> shifts read foobar.ppm
to read resonance assignments from the file foobar.ppm. Chemical shift information in the input file is free-format, organized by residue, one reside record per line. The first two fields of a residue record are the residue type (single letter residue code) and residue number, followed by chemical shifts (hydrogen, heavy atom), ordered by remoteness from the backbone Nitrogen. The number of fields is dependent on the residue type:
 
ALA HN N HA CA HB# CB                        
ARG HN N HA CA HB1,2 CB HG1,2 CG HD1,2 CD                
ASN HN N HA CA HB1,2 CB HD11,12  ND1                    
ASP HN N HA CA HB1,2 CB                        
CYS HN N HA CA HB1,2 CB                        
GLN HN N HA CA HB1,2 CB HG1,2 CG HE11,12 NE1                
GLU HN N HA CA HB1,2 CB HG1,2 CG                    
GLY HN N HA1,2  CA                            
HIS HN N HA CA HB1,2 CB HD2 CD2 HE1 CE1                
ILE HN N HA CA HB CB HG11,HG12 CG1 HD1# CD1 HG2# CG2            
LEU HN N HA CA HB1,2 CB HG CG HD1#,2#  CD1,2  HG2# CG            
LYS HN N HA CA HB1,2 CB HG1,2 CG HD1,2 CD HE1,2  CE            
MET HN N HA CA HB1,2 CB HG1,2 CG HE# CE                
PHE HN N HA CA HB1,2 CB HD1,2 CD1,2 HE1,2 CD1,2 HZ CZ            
PRO     HA CA HB1,2 CB HG1,2 CG HD1,2 CD                
SER HN N HA CA HA1,2 CB                        
THR HN N HA CA HB CB HG2# CG                    
TRP HN N HA CA HB1,2 CB HD1 CD1 HE1 NE1 HZ2 CZ2  HH2  CH2  HZ3  CZ3  HE3  CE3
TYR HN N HA CA HB1,2 CB HD1,2 CD1,2  HE1,2 CE                
VAL HN N HA CA HB CB HG1# CG1 HG2# CG2                

Notes:

  1. If the two shifts in a comma-separated group (e.g. HB1,HB2 in ARG, ASN, ASP,...) are identical, only one value needs to be specified. The two protons will be collected into the pseudoatom group HB#.

  2.  
  3. Assignments in comma-separated groups are assumed to be non-stereospecific. Shifts for non-stereospecifically assigned protons will be marked by a '?' suffix in the labels produced by the label shift command, and the two corresponding pseudoatoms will have the last digit of their names replaced by 't' ("tief") and 'h' ("hoch").

  4.  
  5. For stereospecific assignments a slash ('/') separator should be used instead of the comma (',').

  6.  
  7. The two letter symbol na is used as a place holder for missing data, typically used in the HN and N fields of N-terminal residues.
Example of a resonance assignment file.


A.Widmer, NIBR/CPC/CSG-SB