You can create a user-defined atom list using the Periodic System button from the structure editor.
- Click the Periodic Table button on the structure editor
- Click the Atom List button
- Select the atoms that you wish to include in your atom list
- Click the Ok button. You will see that the atom attached to the cursor has turned to a group of atom symbols encapsulated in brackets.
- Click on the position in your structure in which you would like the atom list to appear
You can use the same tool to create a list of atoms to exclude at a particular position. Follow the same procedure as for the atom list, but choose the Not List button instead of the Atom List button.
You can also perform a similar search, allowing only particular atoms or fragments to appear at a given point in a structure. For example, assume that you wish to search for three distinct substructures in a single search.
- Draw the portion of the molecule that all substructures have in common. This is the parent structure.
- Draw the portions of the molecule that vary in the substructures somewhere to the side of the parent structure but in proximity to one another. These are the fragments.
- Using the Marquis Tool , select all of the fragments that you wish to include in R1. They should be highlighted in green.
- Click on the Smart R-Group button , and type the number of the R-group into the menu. This will automatically assign the fragments that you have selected to that R-group and label them accordingly. Once that is done, click on the place in the parent at which you wish to place the R-group placeholder.
- You will next need to assign the atom on each fragment that is represented by the placeholder R1 in the parent (in other words, the atom that will bond to the parent molecule). Select the Attachment Point button , and then click on the appropriate atom in each fragment.
- If the placeholder R1 bonds to more than one atom in the parent, you need to set a second attachment point, either on the same atom or on a different atom, depending on how you want to attach the fragment. The placeholder may bond to no more than two other atoms in the parent.