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<section id="program-output">
<h1>Program output<a class="headerlink" href="#program-output" title="Link to this heading">¶</a></h1>
<p>As the program runs the key results are written to the screen and recorded
in the file <code class="samp docutils literal notranslate"><span class="pre">xia2.txt</span></code>. This includes everything you should read and includes
appropriate citations for the programs that xia2 has used on your behalf.
There is also a file <code class="samp docutils literal notranslate"><span class="pre">xia2-debug.txt</span></code> which should be send to <a class="reference external" href="mailto:xia2.support%40gmail.com">xia2<span>.</span>support<span>@</span>gmail<span>.</span>com</a>
in the event of program failure. There are also two sensibly named directories,
<code class="samp docutils literal notranslate"><span class="pre">LogFiles</span></code> and <code class="samp docutils literal notranslate"><span class="pre">DataFiles</span></code>, which will be discussed shortly.</p>
<section id="xia2-txt">
<h2>xia2.txt<a class="headerlink" href="#xia2-txt" title="Link to this heading">¶</a></h2>
<p>By design, the program output from xia2 includes only the information that
is critical to read, as will be shown for a 450 image Pilatus 2M data set
recorded from a thaumatin crystal. The results from indexing are displayed
as lattice / unit cell:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="o">-------------------</span> <span class="n">Autoindexing</span> <span class="n">SWEEP1</span> <span class="o">--------------------</span>
<span class="n">All</span> <span class="n">possible</span> <span class="n">indexing</span> <span class="n">solutions</span><span class="p">:</span>
<span class="n">tP</span> <span class="mf">57.60</span> <span class="mf">57.60</span> <span class="mf">149.51</span> <span class="mf">90.00</span> <span class="mf">90.00</span> <span class="mf">90.00</span>
<span class="n">oC</span> <span class="mf">81.45</span> <span class="mf">81.46</span> <span class="mf">149.51</span> <span class="mf">90.00</span> <span class="mf">90.00</span> <span class="mf">90.00</span>
<span class="n">oP</span> <span class="mf">57.59</span> <span class="mf">57.60</span> <span class="mf">149.50</span> <span class="mf">90.00</span> <span class="mf">90.00</span> <span class="mf">90.00</span>
<span class="n">mC</span> <span class="mf">81.46</span> <span class="mf">81.45</span> <span class="mf">149.50</span> <span class="mf">90.00</span> <span class="mf">89.95</span> <span class="mf">90.00</span>
<span class="n">mP</span> <span class="mf">57.60</span> <span class="mf">57.59</span> <span class="mf">149.53</span> <span class="mf">90.00</span> <span class="mf">89.93</span> <span class="mf">90.00</span>
<span class="n">aP</span> <span class="mf">57.59</span> <span class="mf">57.61</span> <span class="mf">149.52</span> <span class="mf">89.93</span> <span class="mf">89.99</span> <span class="mf">89.99</span>
<span class="n">Indexing</span> <span class="n">solution</span><span class="p">:</span>
<span class="n">tP</span> <span class="mf">57.60</span> <span class="mf">57.60</span> <span class="mf">149.51</span> <span class="mf">90.00</span> <span class="mf">90.00</span> <span class="mf">90.00</span>
</pre></div>
</div>
<p>where in each case the solution with the lowest penalty is displayed. The
results of integration are displayed as one character per image - which allows
the overall behaviour of the data to be understood at a glance. While
mostly ’o’ is usually a good indication of satisfactory processing, ’%’ are not
unusual, along with ’.’ for weaker data. If the output consists of mostly ’O’
then it may be helpful to record a low dose data set. The output includes a
convenient legend, and looks like the following:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="o">--------------------</span> <span class="n">Integrating</span> <span class="n">SWEEP1</span> <span class="o">--------------------</span>
<span class="n">Processed</span> <span class="n">batches</span> <span class="mi">1</span> <span class="n">to</span> <span class="mi">450</span>
<span class="n">Integration</span> <span class="n">status</span> <span class="n">per</span> <span class="n">image</span> <span class="p">(</span><span class="mi">60</span><span class="o">/</span><span class="n">record</span><span class="p">):</span>
<span class="n">ooooooooooooooooooooooooooooooooooo</span><span class="o">.</span><span class="n">oooooooooooooooooooooooo</span>
<span class="n">ooooooooooooooooooooooo</span><span class="o">.</span><span class="n">ooooooooooooooooooo</span><span class="o">.</span><span class="n">ooooooo</span><span class="o">.</span><span class="n">oooooooo</span>
<span class="n">ooo</span><span class="o">.</span><span class="n">o</span><span class="o">.</span><span class="n">ooooooo</span><span class="o">.</span><span class="n">oooooooooooooooooooooooooooooooooooooooooooooo</span>
<span class="n">oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo</span>
<span class="n">oooooooooooooooooooo</span><span class="o">.</span><span class="n">ooooooooooooooooooooooooooooooooooooooo</span>
<span class="n">ooooooooooooooooooooooooooooooooooooooooooooooooooo</span><span class="o">.</span><span class="n">oooooooo</span>
<span class="n">ooooooooo</span><span class="o">.</span><span class="n">oooooooooo</span><span class="o">..</span><span class="n">ooo</span><span class="o">.</span><span class="n">oooooooooooooooooooo</span><span class="o">.</span><span class="n">ooooooooooooo</span>
<span class="n">oooooooooooooooooooo</span><span class="o">.</span><span class="n">oooooooo</span><span class="o">.</span>
<span class="s2">"o"</span> <span class="o">=></span> <span class="n">good</span> <span class="s2">"%"</span> <span class="o">=></span> <span class="n">ok</span> <span class="s2">"!"</span> <span class="o">=></span> <span class="n">bad</span> <span class="n">rmsd</span>
<span class="s2">"O"</span> <span class="o">=></span> <span class="n">overloaded</span> <span class="s2">"#"</span> <span class="o">=></span> <span class="n">many</span> <span class="n">bad</span> <span class="s2">"."</span> <span class="o">=></span> <span class="n">blank</span>
<span class="s2">"@"</span> <span class="o">=></span> <span class="n">abandoned</span>
<span class="n">Mosaic</span> <span class="n">spread</span><span class="p">:</span> <span class="mf">0.140</span> <span class="o"><</span> <span class="mf">0.189</span> <span class="o"><</span> <span class="mf">0.290</span>
</pre></div>
</div>
</section>
<section id="html-pages">
<h2>HTML pages<a class="headerlink" href="#html-pages" title="Link to this heading">¶</a></h2>
<p>If xia2html has been run there is a nicely formatted html version of this
report, which includes graphical representation of some of the log file output
from e.g. Aimless. Loading up <code class="samp docutils literal notranslate"><span class="pre">xia2.html</span></code> will give (hopefully self documenting)
results as shown below. If you have manually run xia2,
immediately running xia2html in the same directory will generate this.</p>
<img alt="_images/xia2html.png" src="_images/xia2html.png" />
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