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class="md-content__inner md-typeset" role=main > <section class="tex2jax_ignore mathjax_ignore" id=rugnuxlivemodel > <h1 id=python-client-docs-rugnuxlivemodel--page-root >RugnuxLiveModel<a class=headerlink href="#python-client-docs-rugnuxlivemodel--page-root" title="Link to this heading"></a></h1> <p>What the run made of the model it was given, as the report’s MODEL VALIDATION section states it. The R-factors here are those of the placed model with its own coordinates and B factors; what refinement made of it is in <code class="docutils literal notranslate"><span class=pre >refinement</span></code>. A value that is absent was not computed - the model was not placed, or not by molecular replacement.</p> <section id=properties > <h2 id=properties >Properties<a class=headerlink href="#properties" title="Link to this heading"></a></h2> <table> <thead> <tr class=row-odd ><th class=head ><p>Name</p> <th class=head ><p>Type</p> <th class=head ><p>Description</p> <th class=head ><p>Notes</p> <tr class=row-even ><td><p><strong>placement</strong></p> <td><p><strong>str</strong></p> <td><p>RIGID_BODY (the model fits where it is), MR (molecular replacement placed it) or NOT_PLACED</p> <td><p></p> <tr class=row-odd ><td><p><strong>model_name</strong></p> <td><p><strong>str</strong></p> <td><p></p> <td><p></p> <tr class=row-even ><td><p><strong>predicted</strong></p> <td><p><strong>bool</strong></p> <td><p>Searched for as a predicted model</p> <td><p></p> <tr class=row-odd ><td><p><strong>reason</strong></p> <td><p><strong>str</strong></p> <td><p>Why the model could not be searched for or validated; empty otherwise</p> <td><p></p> <tr class=row-even ><td><p><strong>r_work</strong></p> <td><p><strong>float</strong></p> <td><p></p> <td><p>[optional]</p> <tr class=row-odd ><td><p><strong>r_free</strong></p> <td><p><strong>float</strong></p> <td><p></p> <td><p>[optional]</p> <tr class=row-even ><td><p><strong>cc_model</strong></p> <td><p><strong>float</strong></p> <td><p>Correlation of the merged intensities with the placed model’s, over all reflections</p> <td><p>[optional]</p> <tr class=row-odd ><td><p><strong>fit_sigma</strong></p> <td><p><strong>float</strong></p> <td><p>How far R-work stands below that of the same model in random orientations, in standard deviations</p> <td><p>[optional]</p> <tr class=row-even ><td><p><strong>map_atom_sigma</strong></p> <td><p><strong>float</strong></p> <td><p>Mean 2mFo-DFc value at the atom centres, in map sigma</p> <td><p>[optional]</p> <tr class=row-odd ><td><p><strong>rigid_body_angle_deg</strong></p> <td><p><strong>float</strong></p> <td><p></p> <td><p>[optional]</p> <tr class=row-even ><td><p><strong>rigid_body_shift_a</strong></p> <td><p><strong>float</strong></p> <td><p></p> <td><p>[optional]</p> <tr class=row-odd ><td><p><strong>mr_decision</strong></p> <td><p><strong>str</strong></p> <td><p>Molecular replacement’s decision (AGREES, ENANTIOMORPH, SPACE_GROUP, TWIN_SUBGROUP, or why it placed nothing); empty where it did not run</p> <td><p></p> <tr class=row-even ><td><p><strong>mr_space_group</strong></p> <td><p><strong>str</strong></p> <td><p>The group molecular replacement placed the model in; empty where it placed none</p> <td><p></p> <tr class=row-odd ><td><p><strong>copies</strong></p> <td><p><strong>int</strong></p> <td><p>Copies placed by molecular replacement</p> <td><p>[optional]</p> <tr class=row-even ><td><p><strong>tf_z</strong></p> <td><p><strong>float</strong></p> <td><p>Translation-function Z-score, the highest of the copies’</p> <td><p>[optional]</p> <tr class=row-odd ><td><p><strong>rf_z</strong></p> <td><p><strong>float</strong></p> <td><p>Rotation-function Z-score of the first copy’s orientation</p> <td><p>[optional]</p> <tr class=row-even ><td><p><strong>llg_z</strong></p> <td><p><strong>float</strong></p> <td><p>Likelihood Z-score after the rigid body, where a copy’s translation function did not stand out</p> <td><p>[optional]</p> <tr class=row-odd ><td><p><strong>mr_d_min</strong></p> <td><p><strong>float</strong></p> <td><p>High-resolution limit of the molecular-replacement search, in Angstrom</p> <td><p>[optional]</p> <tr class=row-even ><td><p><strong>anomalous_site</strong></p> <td><p><strong>str</strong></p> <td><p>Atom with the strongest anomalous difference density, e.g. &amp;quot;SG CYS A7&amp;quot;; empty where there is no anomalous map</p> <td><p></p> <tr class=row-odd ><td><p><strong>anomalous_site_sigma</strong></p> <td><p><strong>float</strong></p> <td><p>Anomalous difference density at that atom, in map sigma</p> <td><p>[optional]</p> <tr class=row-even ><td><p><strong>refinement</strong></p> <td><p><a class="reference internal" href=RugnuxLiveRefinement.html ><span class="std std-doc"><strong>RugnuxLiveRefinement</strong></span></a></p> <td><p></p> <td><p>[optional]</p> </table> </section> <section id=example > <h2 id=example >Example<a class=headerlink href="#example" title="Link to this heading"></a></h2> <div class="highlight-python notranslate"><div class=highlight ><pre><span></span><span class=kn >from</span> <span class=nn >jfjoch_client.models.rugnux_live_model</span> <span class=kn >import</span> <span class=n >RugnuxLiveModel</span>
<span class=c1 ># TODO update the JSON string below</span>
<span class=n >json</span> <span class=o >=</span> <span class=s2 >"</span><span class=si >{}</span><span class=s2 >"</span>
<span class=c1 ># create an instance of RugnuxLiveModel from a JSON string</span>
<span class=n >rugnux_live_model_instance</span> <span class=o >=</span> <span class=n >RugnuxLiveModel</span><span class=o >.</span><span class=n >from_json</span><span class=p >(</span><span class=n >json</span><span class=p >)</span>
<span class=c1 ># print the JSON string representation of the object</span>
<span class=nb >print</span><span class=p >(</span><span class=n >RugnuxLiveModel</span><span class=o >.</span><span class=n >to_json</span><span class=p >())</span>
<span class=c1 ># convert the object into a dict</span>
<span class=n >rugnux_live_model_dict</span> <span class=o >=</span> <span class=n >rugnux_live_model_instance</span><span class=o >.</span><span class=n >to_dict</span><span class=p >()</span>
<span class=c1 ># create an instance of RugnuxLiveModel from a dict</span>
<span class=n >rugnux_live_model_from_dict</span> <span class=o >=</span> <span class=n >RugnuxLiveModel</span><span class=o >.</span><span class=n >from_dict</span><span class=p >(</span><span class=n >rugnux_live_model_dict</span><span class=p >)</span>
</pre></div> </div> <p><a class="reference internal" href="../README.html#documentation-for-models"><span class="std std-ref">[Back to Model list]</span></a> <a class="reference internal" href="../README.html#documentation-for-api-endpoints"><span class="std std-ref">[Back to API list]</span></a> <a class="reference internal" href="../README.html"><span class="std std-doc">[Back to README]</span></a></p> </section> </section> </article> </div> </div> </main> </div> <footer class=md-footer > <div class=md-footer-nav > <nav class="md-footer-nav__inner md-grid"> <a href=RugnuxLiveBlob.html title=RugnuxLiveBlob class="md-flex md-footer-nav__link md-footer-nav__link--prev" rel=prev > <div class="md-flex__cell md-flex__cell--shrink"> <i class="md-icon md-icon--arrow-back md-footer-nav__button"></i> </div> <div class="md-flex__cell md-flex__cell--stretch md-footer-nav__title"> <span class=md-flex__ellipsis > <span class=md-footer-nav__direction > "Previous" </span> RugnuxLiveBlob </span> </div> </a> <a href=RugnuxLiveRefinement.html title=RugnuxLiveRefinement class="md-flex md-footer-nav__link md-footer-nav__link--next" rel=next > <div class="md-flex__cell md-flex__cell--stretch md-footer-nav__title"><span class=md-flex__ellipsis > <span class=md-footer-nav__direction > "Next" </span> RugnuxLiveRefinement </span> </div> <div class="md-flex__cell md-flex__cell--shrink"><i class="md-icon md-icon--arrow-forward md-footer-nav__button"></i> </div> </a> </nav> </div> <div class="md-footer-meta md-typeset"> <div class="md-footer-meta__inner md-grid"> <div class=md-footer-copyright > <div class=md-footer-copyright__highlight > &#169; Copyright 2024, Paul Scherrer Institute. </div> Created using <a href="http://www.sphinx-doc.org/">Sphinx</a> 8.1.3. and <a href="https://github.com/bashtage/sphinx-material/">Material for Sphinx</a> </div> </div> </div> </footer> <script src="../../_static/javascripts/application.js"></script> <script>app.initialize({version: "1.0.4", url: {base: ".."}})</script>