Atom lists and NOT lists

MarvinSketch allows you to add Atom List and NOT lists query atoms to your molecule.

An Atom List is a user-defined list of elements included in a structure.

A NOT List is a query atom that allows you to define a list of elements that should not be included in the structure.

Atom List and NOT list can be edited using the Atom label editor tool. For more details click here.

How to create an Atom List

  1. Overwrite an atom
    1.Move your mouse over the appropriate atom of a molecule or make selections on one or multiple atoms.
    2.Type chemical symbols separated by commas, the Atom List replaces the selected atoms.

  2. Edit the atom label by the Atom Label Editor
    1.Select the Atom Label Editor tool.
    2.Click on the atom you want to change.
    3.Type the list. Syntax: [atom1,atom2,...]

  3. Creating a list on the canvas
    1.Move your mouse over the canvas.
    2.Type the atoms you wish to add to the Atom List separated by commas (e.g., au,pt,ag). Backspace can be used to delete errors.
    The Atom List is displayed on the upper left corner of the canvas and concurrently at the tip of the pointer (e.g., L[Au,Pt,Ag]).
    3 Click on the query atom you want to add this Atom List.

  4. You can add Atom Lists to your molecule through the Periodic Table. To add an Atom List to the molecule
    1.Select the Atom List button.
    2.Select the elements you wish to include in the list.
    3.Move the mouse into the canvas and click to add a Query atom representing this atom list.

How to create a NOT List

  1. Overwrite an atom
    1.Move your mouse over the appropriate atom of a molecule or make selections on one or multiple atoms.
    2.Type an exclamation mark first, then start typing chemical symbols separated by commas, the Atom List replaces the selected atoms.

  2. Edit the atom label by the Atom Label Editor
    1.Select the Atom Label Editor tool.
    2.Click on the atom you want to change.
    3.Type the list. Syntax: ![atom1,atom2,...]

  3. Creating a list on the canvas
    1.Move your mouse over the canvas.
    2.Type an exclamation mark first, then type the atoms you wish to add to the NOT Atom List separated by commas (e.g., au,pt,ag). Backspace can be used to delete errors.
    The Atom List is displayed on the upper left corner of the canvas and concurrently at the tip of the pointer (e.g., ~L![A[Au,Pt,Ag]).
    3 Click on the query atom you want to add this NOT Atom List.

  4. You can add NOT Atom Lists to your molecule through the Periodic Table.
    1.Select the NOT List button in the Periodic Table,
    2.Select the elements you wish to include in the list.
    3.Move the mouse into the canvas and click to add a Query atom representing this atom list.