Ambiguity code assignment

This program checks an assigned chemical shifts table for possible "non-unique" assignments: geminal protons or methyl groups, and aromatic atoms on opposite sides of symmetrical rings. For every such atom or group, it asks the user if the assignment is unique. The program's output is the table in NMR-STAR format with ambiguity codes filled in.

Using the program

1. File upload screen.

Select a data table to upload, the appropriate processing options, and then click on the Upload button.

Input data file (example)
The input file must be an ASCII file containing a loop in NMR-STAR v3.1 format, starting with loop_ and ending with stop_. It must contain at least Comp_index_ID, Comp_ID, Atom_ID, and Val columns. If loop does not include the Ambiguity_code and ID (row number) columns, they will be inserted by the program.

The input file must contain data for a single entity. At this time the program can not process tables with data for multiple Entity_ID or Entity_assembly_ID.

Residue codes must be three-letter component identifiers from PDB Component Dictionary (Ligand Expo).

Atom names must follow IUPAC nomenclature. Mx methyl pseudo-atoms are recognized by the program, any other pseudo-atoms will be ignored (but preserved in the output). Non-standard residues also will be ignored but the data preserved in the output.

Output from the BMRB table generator with chemical shift values filled in fit these criteria. To process output from STARch, make sure that atom names are in IUPAC nomenclature as described above (STARch does not attempt any nomenclature conversions).

Processing options
Even an average-sized chemical shifts table can contain a large number of possibly ambiguous assignments leading to a large number of yes/no questions. The processing options can be used to reduce their number.

Flag possible non-unique geminal proton and methyl assignments and Flag possible non-unique symmetrical aromatic ring assignments: if not checked, the program will not flag the corresponding atoms.

Check only these residues field: flag possible non-unique assignments in the specified residues only. To specify residues to check, type in a comma- or space-separated list of residue sequence numbers (Comp_index_ID's) matching those in the uploaded file.

Insert default ambiguity codes applies to all atoms not covered by the above selections. For example, if only Flag possible non-unique geminal proton and methyl assignments is selected, and a residue list is specified, the program will flag geminal atoms and groups in the specified residues. Default ambiguity codes will be inserted for all non-geminal atoms in the specified residues as well as all atoms in all residues not on the list. Default codes are 1 for unique assignments (e.g. backbone atoms, geminal or ring atoms with identical chemical shifts), 2 for geminal atoms that are not stereospecifically assigned, and 3 for ring atoms that are not uniquely assigned.

Overwrite existing ambiguity codes: if checked the program will delete existing ambiguity codes before inserting default ones and flagging possible non-unique ones. If unchecked, the program will ignore atoms that already have an ambiguity code.
Note: STARch has the option to insert default ambiguity codes during file conversion. If your table was generated by STARch with that option on, you'll should check Overwrite existing ambiguity codes here unless you've edited the ambiguity codes in your table.

2. Degenerate assignments screen.

The degenerate assignments screen shows rows where only one atom of a pair has an assigned chemical shift. The format is a table similar to the original NMR-STAR loop, with a yes/no radio button in the rightmost column: is the assignment atom-specific, or does it apply to both atoms. The default for ring atoms is both atoms. There is no default for methylene atoms or Leu and Val methyl groups. If both atoms is selected, the second atom is inserted in the table with the same chemical shift value and both atoms are given ambiguity code 1. If one atom only is selected, the atom is carried over to the next screen. Select an answer for each row and click on "Continue" button.
Note that this page uses JavaScript to force the user to answer all the questions. If you disable JavaScript in your browser and thus bypass the check, any unanswered questions will default to one atom only (i.e. any rows where neither answer is selected will be carried over to the next screen).

3. Ambiguity code assignment screen.

The ambiguity code assignment screen shows atoms flagged by the program in table format similar to the original NMR-STAR loop. The rightmost column contains a yes/no radio button for each flagged atom or group: Stereospecifically assigned? for geminal atoms/groups and Uniquely assigned? for symmetrical aromatic ring atoms. All radio buttons default to "no": ambiguity code 2 for geminal atoms and 3 for ring atoms. Select "yes" for stereospecifically assigned geminal methyls and for ring atoms where it is known which side of the ring is which: they will be given ambiguity code 1. Answer the questions and click on the Generate STAR table button.

4. Output screen.

Use your browser's File - Save As menu to save the resulting NMR-STAR loop.

Notes

• After the output loop is generated, the program deletes the uploaded file. You cannot use the Back button to return to the previous screen and then click on Generate table again: you have to go back to upload screen and re-upload the file.
• The program will automatically renumber rows. Existing row numbers (ID column), if any, will be overwritten.
• If the input file contains "expanded" methyl proton lists, they will be collapsed into one pseudo-atom (e.g. if input had rows for Val HG11, HG12, and HG13, the output will have one row for Val MG1 instead).