Create atom group

(Image projecttree_add_16_h_p)

Often it is convenient to use a unique visualization style or color to highlight a particular set of atoms, or to visualize only a subset of atoms from a molecule. This can be achieved by creating an atom group. Atom groups can be created based on atoms selected in the 3D view or entries selected in the Project Tree. When an atom group has been created, it appears as an entry in the Project Tree in the category "Atom groups". The atoms can then be hidden or shown, and the visualization changed, just as for the molecule entries in the Project Tree.

Note that an atom group entry can be renamed. Select the atom group in the Project Tree and invoke the right-click context menu. Here, the Rename option is found.

Image custom_atom_groups
Figure 12.12: An atom group that has been highlighted by adding a unique visualization style.

Create atom group based on atoms selected in 3D view

When atoms are selected in the 3D view, brown spheres indicate which atoms are included in the selection. The selection will appear as the entry "Current" in the Selections category in the Project Tree.

Once a selection has been made, press the "Create Atom Group" button and a context menu will show different options for creating a new atom group based on the selection:

There are several ways to select atoms in the 3D view:

Image selection_via_showsequences
Figure 12.13: The protein sequence in the split view is linked with the protein structure. This means that when a part of the protein sequence is selected, the same region in the protein structure will be selected.

Create atom group based on entries selected in the Project Tree

Select one or more entries in the Project Tree, and press the "Create Atom Group" button, then a context menu will show different options for creating a new atom group based on the selected entries:

If a Binding Site Setup is present in the Project Tree (A Binding Site Setup could only be created using the now discontinued CLC Drug Discovery Workbench), and entries from the Ligands or Docking results categories are selected, two extra options are available under the header Create Atom Group (Binding Site). For these options, atom groups are created considering all molecules included in the Binding Site Setup, and thus not taking into account which Project Tree entries are currently visible.