This popup contains a table of all of the assignable atoms and atom groups for a specified molecule and chain, and provides the primary means of viewing assigments and specifying atom and spin system assignments in conjunction with the Assignment: Assignment Panel popup.

Atom Table

The {Atom table} tab lists all the atoms present in the selected molecular chain. The information and appearance of the table depends on the selection of the elements and residues, and options set in the {Options} tab. Assigned atoms are indicated with dark colors.

Selection of atoms activates options to remove assignments or show the peaks that were assigned to the selected atoms. When using the [Assign Resonance] button in the Assignment: Assignment Panel popup, the atom assignment is made by selecting the atom from this atom table.

The Molecules: Atom Browser popup (Atom Table).

Chain

Specifies the chain to be listed in the table.

Residue

Specifies which residues to show in the table. The user can show all residues, or only specific residues.

Nucleotides

Specifies the way the atoms of the nucleotides are shown:

• • Interlaced:

  • Lists base and sugar atoms in interlaced separate rows, appending nucleotide numbers with b and s, respectively.

  • Base:

  • Lists only the atoms in the base of the nucleotide.

  • Sugar-P:

  • Lists only the atoms in the sugar ring and phosphate backbone of the nucleotide.

  • Long Row:

  • Lists all atoms in one long row.

Elements

The element buttons specify which elements are shown in the table. Buttons of shown elements are colored.

Atom Table table

This is the actual table in which all the atoms are listed. The atom columns are variable and depend on the residue and element selections.

#

The residue number.

Residue

The residue name.

Set ring flip equivalency

When an aromatic residue is selected that contains potentially equivalent atoms in symmetric aromatic rings (due to ring rotation, e.g. PHE, TYR), this option can be used to change the equivalency status.

Equivalent atoms give rise to one resonance, whereas non-equivalent atoms give rise different resonances. For example, with fast rotation delta carbon atoms of tyrosine will become one equivalent set Cd* (has one resonance), otherwise they will be to sets Cd1 and Cd2 (two resonances).

Selection of an aromatic residue in the |Residue| column changes the button to [Make ..... ring non-equivalent] or [Make ..... ring equivalent], depending on the current equivalency status.

Remove atom assignments

Removes the atom assignments of the selected atom.

Show peaks

Shows all the peaks that contain resonances that are assigned to the selected atom using the Peaks: Selected Peaks popup.

Options

Edit documentation here.

Prochirals

This frame lists the options for displaying prochiral atoms, such as Valine Cg's or Glu Hb's.

Non-Stereospecific

If selected, displays all the non-stereospecifically assigned prochiral atoms. The table displays the atoms as options with an undefined spatial arrangement. For example Ser Hb options would be Hba and Hbb. Here, a resonance assigned to Hba may represent either Hb2 or Hb3 in a structure (but not both). If Hbb is also assigned it would represent the remaining beta proton whatever its stereochemistry.

Stereospecific

If selected, displays all the stereospecifically assigned prochiral atoms as options with a specified spatial arrangement using IUPAC nomenclature. For example Ser Hb options would be Hb2 and Hb3.

Ambiguous

If selected, displays atom sets that are equivalent to the selection of two or more other atom sets, and thus provides a concept similar to pseudoatoms. This option is useful for assigning to prochiral atom sets which have unresolvable chemical shifts. For example assigning a peak to Ser Hb* is the same as assigning to both Hb2 and Hb3. In this case the peak is assigned to two different resonances (Hb2,Hb3) with very similar chemical shifts.

Assignment Status

This frame lists the options for displaying atoms based on their assignment status, and the chemical shift list selection.

assignSelect

The assign select frame. Assignment status selection options are:

• • Any

  • Assigned

  • Unassigned

  • Tentative

Shift List

Specifies the chemical shift list from which the assignment status is used.

Isotope Labelling

This frame lists the isotope options.

Min Isotope Fraction

Specifies the minimum isotope fraction in the selected labelling scheme.

Scheme

Selects the isotope labelling scheme to be used for the prediction of the peaks. See also Molecules: Isotopomer Schemes.