Graphical entities have an active selection. In essence this selection is a subset of atoms, residues, chains and bonds. The active selection is displayed with a green halo around the structure. The selection can be set either programmatically by using Entity::SetSelection() or interactively by using the selection tool.
eh=io.LoadEntity("fragment.pdb") go=gfx.Entity("test",eh.CreateFullView()) ev = eh.Select(mol.Query("rnum=2,3,8,13")) go.SetSelection(ev) go.SetRenderMode(gfx.RenderMode.CUSTOM) go.SetColor(gfx.YELLOW,"(ele=C and rnum=1:4)") scene.Add(go) scene.SetCenter(go.GetCenter()) scene.AutoslabMax()