Reorder Atoms Dialog Box

Reorder the atom numbers in a comparison structure to match the ordering in a reference structure either automatically or by manual selection on two diagrams or from two lists. The name of this dialog box and the options present may vary according to the location from which it is opened.

  • Using
  • Features
  • Additional Resources

Using the Reorder Atoms Dialog Box

There are several ways in which you can use this dialog box to map the atoms of the comparison structure to those of the reference structure.

  1. Use the automated detection (guess) tools. Select a guess method and click Guess. The guessed atoms are marked in light blue. If the guess is good, click Accept Guess; if not, click Reject Guess. The atoms are marked in green if the guess is accepted; if it is rejected the markers are removed.

  2. Pick corresponding atoms in the Workspace, which is tiled with the reference structure on the left and the comparison structure on the right. First, pick a reference atom, which is highlighted. Then pick the corresponding comparison atom; the suggested atom is highlighted. The atoms are marked with green markers.

  3. Pick corresponding atoms in the two diagrams. First, pick a reference atom, which is then marked with a yellow square. Then pick the corresponding comparison atom. The atoms are marked with green markers.

  4. Pick corresponding atoms in the two lists, reference first. The atoms are also marked in the diagrams when you pick them.

If you make a mistake in the mapping, you can simply select the mis-mapped atom in the reference diagram or list, and then select the correct atom in the comparison diagram or list.

If you want to clear the entire mapping and start over, click Clear Mapping or Undo All Mapping.

Reorder Atoms Dialog Box Features

Guess method section

Choose a guess method for automatically mapping the atom numbers of the comparison structure to match the reference structure.

Monatomic elements option

Map atoms for elements that only occur once in the reference structure and in the comparison structure.

Unique SMILES order - conformers only option

Map atoms on the basis of the order in the unique SMILES string for the entire reference structure or comparison structure. The reference structure and the comparison structure must be conformers (no changes in bonding). This method might not be able to determine the mapping of hydrogen atoms.

SMARTS patterns of whole molecule or unique atoms option

Map atoms on the basis of SMARTS patterns, either of individual atoms or of whole molecules. If a SMARTS pattern has only one match in the reference structure and one match in the comparison structure, use that pattern to map the atom numbers. The SMARTS patterns for unique atoms identify individual atoms solely on the basis of their bonding pattern, with no account taken of the identity of the atoms to which they are bonded.

Based on the 3D structures option and Threshold text box

Superimpose the comparison structure on the reference structure, and map each comparison atom to the closest reference atom of the same element. Specify the threshold distance for the closest reference atom in the text box, in angstroms. If there is no nearby atom of the same element that falls within the threshold distance specified, the mapping of the atom is not done. This method uses the unit cell for superposition.

Use all methods option

Use all of the applicable methods to determine the mapping between the reference and comparison atoms.

Guess buttons

Use these buttons to apply the guess method to determine atom mappings.

  • Guess—Click this button to identify corresponding atoms based on the guess method. The identified atoms are marked in blue on the diagrams. Once a guess is made, you must either accept or reject it before any other mappings can be made.

  • Accept Guess—Accept the current guess as the correct mapping. The identified atoms are marked in green on the diagrams.

  • Reject Guess—Reject the current guess as an incorrect mapping. The blue markers are removed from the diagrams.

Automatically map hydrogens and monatomic elements option

Whenever a change is made to the mapping, any hydrogens attached to mapped atoms are mapped if possible, and any remaining atoms that are the only remaining unmapped instances of an element are also mapped. The mapping of hydrogens is done as follows:

  • If the reference atom and the corresponding comparison atom have only one hydrogen, that hydrogen is mapped.

  • If the reference atom and the corresponding comparison atom have the same number of hydrogens (more than one), and the dihedral angles for the hydrogens in the reference structure can be matched to dihedral angles for the hydrogens in the comparison structure, the hydrogens are mapped.

Pick reference and comparison atom pairs in Workspace option

Pick pairs of reference and comparison atoms in the Workspace, reference first, then comparison. The reference and comparison structures are shown in the Workspace in a tiled view with the entry titles shown. When you pick a reference atom in the left tile, it is highlighted in the Workspace, and the suggested comparison atom is also highlighted in the right tile, in a different color. The picked atoms are also highlighted in the panel. Likewise, if you pick atoms in the lists, they are highlighted in the Workspace.

2D structure displays

The 2D structures are only shown when reordering atoms for the Reaction Path Interpolation Panel. The displays show 2D images of the structures, which you can use for mapping comparison atoms to reference atoms. The atom numbering is indicated on the structure, and the numbers are colored by element. Atoms that are mapped are marked with a green sphere; atoms for which the mapping has been guessed but not yet accepted are marked with light blue spheres.

Reference structure display

This area displays the 2D structure of the reference. You can select an atom to start defining a mapping. The atom can be an unmapped atom or it can be an already mapped atom. The selected atom is marked with a yellow square. If you pause the pointer over a mapped atom, it is marked with a green square, and the mapped atom in the comparison structure is also marked with a green square. This also happens if you select a mapped atom, which allows you to identify which atom it is currently mapped to.

Comparison structure display

This area displays the 2D comparison structure. You can select an atom to complete the mapping to the atom selected in the reference structure. The reference atom and the selected atom are marked in green and the yellow square is removed from the reference atom. If you pause the pointer over a mapped atom, it is marked with a green square, and the mapped atom in the reference structure is also marked with a green square.

Atom lists

These lists show the atom numbering in the reference and the comparison structure, with the element label first and the atom number next. The reference rows are terminated with a dash prior to mapping; the mapped comparison atom number is added after the dash when a reference atom is mapped. Rows for unmapped atoms are colored white; rows for mapped atoms are colored green; rows for guessed mappings are colored light blue.

When you select a row in the reference atom list, it is selected and marked in the diagram or the Workspace. When you select a row in the comparison atom list, it is mapped to the selected atom in the reference atom list, the two rows are colored green and the atoms are highlighted in the diagram or the Workspace.

Undo Selected Mapping button

Undo the selected mapping. To select a mapping, click the reference atom and the corresponding comparison atom. This allows you to remove a mapping. To fix an incorrect mapping, you can also simply select the reference atom and the correct comparison atom. Only present from the Reorder Final Structure Atoms Dialog Box.

Undo All Mappings button

Undo the entire mapping. All markers are removed, and all comparison atom numbers are removed from the reference atom list. Only present from the Reorder Final Structure Atoms Dialog Box.

Hide Mapped Atoms button

Hide the mapped atoms in the Workspace to more easily see which atoms have not been mapped. This button only works if the Pick reference and comparison atom pairs in Workspace option is selected. Only present from the Reorder Final Structure Atoms Dialog Box.

Show All Atoms button

Show the mapped atoms that were hidden in the Workspace from using the Hide Mapped Atoms button. Only present from the Reorder Final Structure Atoms Dialog Box.

Clear Mapping button

Clear the entire mapping. All markers are removed, and all comparison atom numbers are removed from the reference atom list. Only present from the Reorder Product Atoms Dialog Box.

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