TALOS and BMRB format chemical shift tables

NMRPipe/TALOS Chemical shift Table Sample

Descriptions

REMARK Chemical Shift Table for ubiquitin

DATA FIRST_RESID 1

DATA SEQUENCE MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL
DATA SEQUENCE EDGRTLSDYN IQKESTLHLV LRLRGG

VARS   RESID RESNAME ATOMNAME SHIFT

FORMAT %4d   %1s     %4s      %8.3f

   1 M   CB   33.270
   1 M   CA   54.450
   1 M    C  170.540
   1 M   HA    4.230
   2 Q   HN    8.900
   2 Q   CA   55.080
   2 Q   CB   30.760
   2 Q    C  175.920
   2 Q   HA    5.249
   2 Q    N  123.220
   3 I   HA    4.213
   3 I    C  172.450
   3 I   CA   59.570
   3 I    N  115.340
   3 I   HN    8.320
   3 I   CB   42.210
   ...

REMARK lines (optional): comments and remarks

DATA FIRST_RESID line (optional, default = 1): specifies the first residue ID for the sequence provided in DATA SEQUENCE lines

DATA SEQUENCE line(s) (required): specifies the complete (one-letter) amino acid sequence

VARS line (required): labels the column names (variables)

the names are case-sensitive
required variable columns are: RESID RESNAME ATOMNAME SHIFT
specified in any order, other columns are ignored

FORMAT line (required): specifies the column data type

follows those used by UNIX/C "printf" function:

%d for integers
%f for floating-point values
%s for text

must be specified in same order as columns defined in VARS line

Chemical shift data lines (required):

columns are space-separated
no individual item in the table may contain spaces
no all-blank values are allowed
RESID column: integer value for residue number
RESNAME column: text value for residue name

one-letter or three-letter amino acid names
should match the corresponding residue type in the DATA SEQUENCE specification

ATOMNAME column: text value for atom name
SHIFT column: floating-point value for chemical shift

BMRB NMR-Star v2.1 Chemical shift Table Sample

Descriptions

   _Mol_residue_sequence                       
;
MQIFVKTLTGKTITLEVEPS
DTIENVKAKIQDKEGIPPDQ
QRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG
;

   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  1 MET HA   H   4.230 . . 
        5  1 MET C    C 170.54  . . 
        6  1 MET CA   C  54.45  . . 
        7  1 MET CB   C  33.27  . . 
       10  2 GLN H    H   8.90  . . 
       11  2 GLN HA   H   5.249 . . 
       17  2 GLN C    C 175.92  . . 
       18  2 GLN CA   C  55.08  . . 
       19  2 GLN CB   C  30.76  . . 
       21  2 GLN N    N 123.22  . . 
       23  3 ILE H    H   8.32  . . 
       29  3 ILE C    C 172.45  . . 
       30  3 ILE CA   C  59.57  . . 
       31  3 ILE CB   C  42.21  . . 
       35  3 ILE N    N 115.34  . . 
       .
       .
       .
   stop_

Standard BMRB NMR-Star v2.1 format chemical shift files, such as those downloaded from BMRB website, are accepted. Otherwise, a chemical shift data file with the following minimal requirments (of BMRB NMR-Star v2.1 format) is also allowed:

Full amino acid sequence definition section (optional):

this section is strongly recommended
_Mol_residue_sequence label is required for this section
sequence data must be capped by two ";" lines
only the one-letter amino acid name is allowed
the residue number of first residue must be 1

Chemical shift data section (required):

columns are space-separated
no individual item in the table may contain spaces
no all-blank values are allowed (use "." if needed)
must be capped by a "loop_" and a "stop_" line
column names must be specified before the data section and (immediately) after the "loop_" line
the following column names are required (and could be with random order):

_Residue_seq_code: integer value for residue number
_Residue_label: text value for three-letter residue name
_Atom_name: text value for atom name
_Chem_shift_value: floating-point value for chemical shift

if the "Full amino acid sequence definition section" is not provided, the full amino acid sequence will be re-stored from the data section

residue name of "?" will be assigned to residues without chemical shift data

BMRB NMR-Star v3.1 Chemical shift Table Sample

Descriptions

   _Entity.Polymer_seq_one_letter_code      
;
MQIFVKTLTGKTITLEVEPS
DTIENVKAKIQDKEGIPPDQ
QRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG
;

   loop_
      _Entity_comp_index.ID
      _Entity_comp_index.Auth_seq_ID
      _Entity_comp_index.Comp_ID
      _Entity_comp_index.Comp_label
      _Entity_comp_index.Entry_ID
      _Entity_comp_index.Entity_ID

       1 . MET . 6457 1 
       2 . GLN . 6457 1 
       3 . ILE . 6457 1 
       4 . PHE . 6457 1 
       5 . VAL . 6457 1 
       6 . LYS . 6457 1 
       7 . THR . 6457 1 
       8 . LEU . 6457 1 
       9 . THR . 6457 1 
      10 . GLY . 6457 1 
      ...

   stop_

   loop_
      _Atom_chem_shift.ID
      _Atom_chem_shift.Assembly_atom_ID
      _Atom_chem_shift.Entity_assembly_ID
      _Atom_chem_shift.Entity_ID
      _Atom_chem_shift.Comp_index_ID
      _Atom_chem_shift.Seq_ID
      _Atom_chem_shift.Comp_ID
      _Atom_chem_shift.Atom_ID
      _Atom_chem_shift.Atom_type
      _Atom_chem_shift.Atom_isotope_number
      _Atom_chem_shift.Val
      _Atom_chem_shift.Val_err
      _Atom_chem_shift.Assign_fig_of_merit
      _Atom_chem_shift.Ambiguity_code
      _Atom_chem_shift.Occupancy
      _Atom_chem_shift.Resonance_ID
      _Atom_chem_shift.Auth_entity_assembly_ID
      _Atom_chem_shift.Auth_asym_ID
      _Atom_chem_shift.Auth_seq_ID
      _Atom_chem_shift.Auth_comp_ID
      _Atom_chem_shift.Auth_atom_ID
      _Atom_chem_shift.Details
      _Atom_chem_shift.Entry_ID
      _Atom_chem_shift.Assigned_chem_shift_list_ID

        1 . 1 1  1  1 MET HA   H  1   4.230 . . . . . . . . MET HA   . 6457 1 
        2 . 1 1  1  1 MET HB2  H  1   2.08  . . . . . . . . MET HB2  . 6457 1 
        3 . 1 1  1  1 MET HG2  H  1   2.02  . . . . . . . . MET HG2  . 6457 1 
        4 . 1 1  1  1 MET HE1  H  1   1.663 . . . . . . . . MET HE   . 6457 1 
        5 . 1 1  1  1 MET HE2  H  1   1.663 . . . . . . . . MET HE   . 6457 1 
        6 . 1 1  1  1 MET HE3  H  1   1.663 . . . . . . . . MET HE   . 6457 1 
        7 . 1 1  1  1 MET C    C 13 170.54  . . . . . . . . MET C    . 6457 1 
        8 . 1 1  1  1 MET CA   C 13  54.45  . . . . . . . . MET CA   . 6457 1 
        9 . 1 1  1  1 MET CB   C 13  33.27  . . . . . . . . MET CB   . 6457 1 
       10 . 1 1  1  1 MET CG   C 13  30.95  . . . . . . . . MET CG   . 6457 1 
       11 . 1 1  1  1 MET CE   C 13  17.86  . . . . . . . . MET CE   . 6457 1 
       12 . 1 1  2  2 GLN H    H  1   8.90  . . . . . . . . GLN H    . 6457 1 
       13 . 1 1  2  2 GLN HA   H  1   5.249 . . . . . . . . GLN HA   . 6457 1 
       14 . 1 1  2  2 GLN HB2  H  1   1.87  . . . . . . . . GLN HB2  . 6457 1 
       15 . 1 1  2  2 GLN HB3  H  1   1.687 . . . . . . . . GLN HB3  . 6457 1 
       16 . 1 1  2  2 GLN HG2  H  1   1.81  . . . . . . . . GLN HG2  . 6457 1 
       17 . 1 1  2  2 GLN HE21 H  1   7.65  . . . . . . . . GLN HE21 . 6457 1 
       18 . 1 1  2  2 GLN HE22 H  1   6.79  . . . . . . . . GLN HE22 . 6457 1 
       19 . 1 1  2  2 GLN C    C 13 175.92  . . . . . . . . GLN C    . 6457 1 
       20 . 1 1  2  2 GLN CA   C 13  55.08  . . . . . . . . GLN CA   . 6457 1 
       21 . 1 1  2  2 GLN CB   C 13  30.76  . . . . . . . . GLN CB   . 6457 1 
       22 . 1 1  2  2 GLN CG   C 13  34.63  . . . . . . . . GLN CG   . 6457 1 
       23 . 1 1  2  2 GLN N    N 15 123.22  . . . . . . . . GLN N    . 6457 1 
       24 . 1 1  2  2 GLN NE2  N 15 111.95  . . . . . . . . GLN NE2  . 6457 1 
       25 . 1 1  3  3 ILE H    H  1   8.32  . . . . . . . . ILE H    . 6457 1 
       .
       .
       .
   stop_

Standard BMRB NMR-Star v3.1 format chemical shift files, such as those downloaded from BMRB website, are accepted. Otherwise, a chemical shift data file with the following minimal requirments (of BMRB NMR-Star v3.1 format) is also allowed:

Full amino acid sequence (one-letter) definition section (optional):

this section is strongly recommended
_Entity.Polymer_seq_one_letter_code label is required for this section
sequence data must be capped by two ";" lines
only the one-letter amino acid name is allowed
the residue number of first residue must be 1

Full amino acid sequence (three-letter) definition section (optional):

this section is alternative to the one-letter full amino acid sequence definition secton
columns are space-separated
no individual item in the table may contain spaces
no all-blank values are allowed (use "." if needed)
must be capped by a "loop_" and a "stop_" line
the following column names are specified:

_Entity_comp_index.ID: integer value for residue number
_Entity_comp_index.Comp_ID: text value for three-letter residue name

Chemical shift data section (required):

columns are space-separated
no individual item in the table may contain spaces
no all-blank values are allowed (use "." if needed)
must be capped by a "loop_" and a "stop_" line
column names must be specified before the data section and (immediately) after the "loop_" line
the following column names are required (and could be with random order):

_Atom_chem_shift.Entity_ID: integer number of 1 for Entity ID
_Atom_chem_shift.Seq_ID: integer value for residue number
_Atom_chem_shift.Comp_ID: text value for three-letter residue name
_Atom_chem_shift.Atom_ID: text value for atom name
_Atom_chem_shift.Val: floating-point value for chemical shift

if the "Full amino acid sequence definition section" is not provided, the full amino acid sequence will be re-stored from this section

residue name of "?" will be assigned to residues without chemical shift data