Click on the protein and drag the click to right and the then the left. Click on the protein and drag the click up and down. The RasMol Command Line screen should appear and should contain a blicking cursor within it. Note that the 33 selected atoms are now displayed in spacefilling mode while the rest of the protein is still in the wireframe mode. These 33 atoms are a ligand which is bound to the protein.
Ligands can be any molecule or ion which binds specifically to a protein for a particular purpose.
Zoom in on the 33 selected spacefilling atoms until you can place your cursor directly over one of the gray spacefilling atoms. Click on the gray spacefilling atom. This text means that you clicked on the number 6 carbon atom which is part of a ATP molecule which is bound to the protein. Note that the color of the selected atoms has changed. Look in the RasMol Command Line to see an identification of the amino acid that you just clicked on.