This is a generic input format, where each line contains data for one atom and values are separated by whitespace (spaces and/or tabs). Many spreadsheet programs, such as Microsoft Excel, can export data in this format (often called "tab-delimited" file). Other applications produce files very similar to this format: Sparky output, for example, can be converted using this format.
Each line contains following values: chemical shift id, residue sequence
number, residue label, atom name, type, chemical shift value, chem. shift
value error, chem. shift ambiguity code. Residue label and sequence must
be present, the rest is optional. Residue label and sequence code may be
stored in one column, e.g. C11.
To convert this format, you will need to add column headers in the first line of the file. You may have to rename the columns (if headers are already present), and delete columns that have no corresponding fields in NMR-STAR (such as standard deviation in Sparky output). Also, make sure to put non-blank character(s) (e.g. a dash, or "n/a") in place of missing values.
First line may contain the number of fields (columns) in the file. This number was required by old version of STARch. Current version does not need this number, but it is supported for backwards compatibility.
Second line (or first, if column count is omitted) must contain space/tab-separated list of field names. Field name must be one of the following:
| shift_id | Chemical shift id |
| seq_code | Residue sequence code |
| seqCode_label | Residue label and sequence code together, e.g. C11.
You must use 1-letter residue label in this field, and
it must be the first character in the string |
| label | Residue label. |
| name | Atom name. |
| type | Atom type. |
| value | Chemical shift value. |
| value_error | Error in chemical shift value. |
| ambiguity_code | Chemical shift ambiguity code. |
| nothing | Comment or other extra information. |
Nothing field will be printed out as NMR-STAR comment.
Shift_id column is ignored, STARch re-numbers table rows
on output.
seqCode_label and label
(or seq_code), STARch will complain about duplicate residue
labels/numbers and refuse to convert the file.
Third and following lines contain space-separated field values, one record (atom) per line.
Note that you must put something (e.g. a dash or "n/a") in place of missing values, unless it's in the last (rightmost) column.
seq_code label name value value_error nothing 1 GLU NN 120.20 .01 XYZ 1 GLU CA 57.19 . 1 GLU CB 28.16 1 GLU CG 34.23 1 GLU HN n/a 1 GLU HA 3.82 1 GLU QB 2.06 1 GLU HG+ 2.41 n/a comment 1 GLU HG- 2.34
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 GLU NN . 120.20 .01 . # XYZ 2 1 GLU CA . 57.19 . . # shift err. = . 3 1 GLU CB . 28.16 . . # shift err. = null 4 1 GLU CG . 34.23 . . # shift err. = null 5 1 GLU HN . . . . # shift val. = n/a shift err. = null 6 1 GLU HA . 3.82 . . # shift err. = null 7 1 GLU QB . 2.06 . . # shift err. = null 8 1 GLU HG+ . 2.41 . . # shift err. = n/a comment 9 1 GLU HG- . 2.34 . . # shift err. = null stop_
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 GLU H H . . . # shift val. = n/a shift err. = null 2 1 GLU N N 120.20 .01 . # XYZ 3 1 GLU CA C 57.19 . . # shift err. = . 4 1 GLU HA H 3.82 . . # shift err. = null 5 1 GLU C C . . . 6 1 GLU CB C 28.16 . . # shift err. = null 7 1 GLU HB2 H 2.06 . ? # shift err. = null 8 1 GLU HB3 H . . . 9 1 GLU CG C 34.23 . . # shift err. = null 10 1 GLU HG2 H . . . 11 1 GLU HG3 H . . . 12 1 GLU CD C . . . 13 1 GLU HE2 H . . . 14 1 GLU HG+ . 2.41 . . # shift err. = n/a comment Invalid atom 15 1 GLU HG- . 2.34 . . # shift err. = null Invalid atom stop_
Last updated: Fri 02 Jul 2004 05:16:53 PM CDT