s="k">def</span> <span class="nf">_write_pymol_commands</span><span class="p">(</span><span class="n">commands</span><span class="p">,</span> <span class="n">output_file</span><span class="p">):</span>
    <span class="sd">&quot;&quot;&quot;</span>
<span class="sd">    Helper function to write a set of lines to a file</span>

<span class="sd">    Parameters</span>
<span class="sd">    ----------</span>
<span class="sd">    commands : list(str)</span>
<span class="sd">        List of commands, each will be w