class="c1"># at the end we also need to issue a rebuild so</span>
    <span class="c1"># the changes are displayed</span>
    <span class="n">cmds</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s2">&quot;rebuild&quot;</span><span class="p">)</span>

    <span class="n">_write_pymol_commands</span><span class="p">(</span><span class="n">cmds</span><span class="p">,</span> <span class="n">output_file</span><span class="p">)</span>
    <span class="k">return</sp