Assigned Chemical Shift File Help
Resources for helping to generate NMR-STAR 3.2 chemical shift tables
Although complete NMR-STAR 3.2 files, which may contain more information than just assigned chemical shifts, are accepted, this page only documents how to create a file that contains just a NMR-STAR 3.2 assigned chemical shift loop.- Star Conversion Handler (STARch): A tool for converting some common software packages' data files into NMR-STAR 3.2 loops.
- Atom Table generator: A tool for creating an initial stub chemical shift table given a biopolymer sequence string, which is then ready to have the chemical shift values populated into it.
Example Assigned Chemical Shifts
The assigned chemical shifts loop is a table of data in an ASCII file that must fit the following format. (See the section below inside the boxes for examples.)- Whitespace separates terms. Spaces and tabs are treated as equivalent. To include a space in a value, the value must be in quotes (".. ..").
- The keyword loop_ begins the table. The keyword stop_ ends the table. The stop_ at the end of the loop is optional.
- The table begins with a list of the header tags defining the columns. Columns can be in any order, but the header tags must be there to define which column is which. The first header tag in the list defines the first column of data that will appear below in the table. The second header tag in the list defines the second column of data, and so on.
- Header tag names must start with an underscore character ('_'). If the underscore is left off, it will look like a value and will be misinterpreted to be the start of the data for the table.
- Use the exact tag names as described in the examples below - spelled as shown, capitalized as shown.
- The list of columns must match the data in the table. For example, if there are 10 columns in the data, but 11 header tags, this will generate an error.
- Every row of data must have the same number of values. If a particular value is not populated for some rows of data, then you must use a period character (.) in that column to indicate a null value for that row for that column. If you leave that value blank, then the mismatch between the header and the data will generate an error.
- The "Ambiguity_code" column is filled with a number describing the type of ambiguity there is for this row of data. The numerical codes are defined below.
Chemical Shift Ambiguity Index Value Definitions
The values other than 1 are used for those atoms with different
chemical shifts that cannot be assigned to stereospecific atoms
or to specific residues or chains.
Index Value Definition
1 Unique (including isolated methyl protons, geminal atoms, and geminal methyl
groups with identical chemical shifts) (e.g. ILE HD11, HD12, HD13 protons)
2 Ambiguity of geminal atoms or geminal methyl proton groups (e.g. ASP HB2 and HB3
protons, LEU CD1 and CD2 carbons, or LEU HD11, HD12, HD13 and HD21, HD22,
HD23 methyl protons)
3 Aromatic atoms on opposite sides of symmetrical rings (e.g. TYR HE1 and HE2
protons)
4 Intraresidue ambiguities (e.g. LYS HG and HD protons or TRP HZ2 and HZ3 protons)
5 Interresidue ambiguities (LYS 12 vs. LYS 27)
6 Intermolecular ambiguities (e.g. ASP 31 CA in monomer 1 and ASP 31 CA in monomer 2
of an asymmetrical homodimer, duplex DNA assignments, or other assignments
that may apply to atoms in one or more molecule in the molecular assembly)
9 Ambiguous, specific ambiguity not defined
EXAMPLE 1:
#
# Everything from a hash-character ('#') to the end of a line is
# a comment that is ignored. This is an example of a comment.
#
loop_
_Atom_chem_shift.ID # Row number
_Atom_chem_shift.Entity_assembly_ID # Defines the polymer chain
_Atom_chem_shift.Comp_index_ID # Residue number
_Atom_chem_shift.Comp_ID # Residue label
_Atom_chem_shift.Atom_ID # Atom name
_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 # For the meaning of this , see above.
#
# Entity Comp Atom Assign. Atom
# Assembly index Comp Atom Atom isot. Val fig. of Ambig.
# ID ID ID ID ID type num Val err merit code
#----------------------------------------------------------------------------
#
#
1 1 1 GLY HA2 H 1 4.065 0.02 . 2
2 1 1 GLY HA3 H 1 4.192 0.02 . 2
3 1 1 GLY CA C 13 44.876 0.30 . 1
4 1 2 SER H H 1 8.933 0.02 . 1
5 1 2 SER HA H 1 4.653 0.02 . 1
6 1 2 SER HB2 H 1 4.057 0.02 . 2
7 1 2 SER HB3 H 1 4.071 0.02 . 2
8 1 2 SER C C 13 175.530 0.30 . 1
9 1 2 SER CA C 13 57.162 0.30 . 1
10 1 2 SER CB C 13 65.356 0.30 . 1
11 1 2 SER N N 15 118.407 0.30 . 1
stop_ # This marks the end of the table.
# ---- (This example only shows the first two residues in the list.) ---
However, not every column is mandatory as BMRB can fill in some of them by inference during annotation. Below is an example of a minimal chemical shifts file with some of the columns left out, which would be accepted by the BMRBdep system:
EXAMPLE 2: Minimal example with some optional tags left off.
# A Minimal example with some optional columns removed
loop_
_Atom_chem_shift.ID
_Atom_chem_shift.Entity_assembly_ID
_Atom_chem_shift.Comp_index_ID
_Atom_chem_shift.Comp_ID
_Atom_chem_shift.Atom_ID
_Atom_chem_shift.Atom_isotope_number
_Atom_chem_shift.Val
_Atom_chem_shift.Val_err
1 1 1 GLY HA2 1 4.065 0.02
2 1 1 GLY HA3 1 4.192 0.02
3 1 1 GLY CA 13 44.876 0.30
4 1 2 SER H 1 8.933 0.02
5 1 2 SER HA 1 4.653 0.02
6 1 2 SER HB2 1 4.057 0.02
7 1 2 SER HB3 1 4.071 0.02
8 1 2 SER C 13 175.530 0.30
9 1 2 SER CA 13 57.162 0.30
10 1 2 SER CB 13 65.356 0.30
11 1 2 SER N 15 118.407 0.30
stop_