tiple chains are present in the structure.</span>
<span class="sd">    atom : str, optional (default: None)</span>
<span class="sd">        Only apply mapping to this atom in each residue</span>

<span class="sd">    Returns</span>
<span class="sd">    -------</span>
<span class="sd">    cmds : list</span>
<span class="sd">        List of generated pymol commands (written to output_file)</span>
<span class="sd">    &quot;&quot;&quot;</span>
    <span class="n">cmds</span> <span class="o">=</span> <span clas