Phoenix ELN 3.1.1

Author: abrechts

Phoenix ELN Help.hnd

@@ -201,20 +201,20 @@ <h2>Reaction Searches</h2>
 <p class="rvps3"><img alt="" style="width : 626px; height : 164px; padding : 1px;" src="lib/RSS-QueryPart.jpg"></p>
 <p class="rvps3"><span class="rvts8"><br/></span></p>
 <p class="rvps3"><span class="rvts8">A reaction substructure query describes the relevant parts which effectively change during the conversion between reactant and product, plus substituents in their nearest neighborhood relevant for restricting the query towards specific geometric arrangements (e.g. for distinguishing primary, secondary or tertiary alcohols). Please note that in </span><span class="rvts17">Phoenix ELN</span><span class="rvts8"> there’s no need to explicitly assign reaction centers for this.</span></p>
-<p class="rvps33"><img alt="" style="width : 654px; height : 298px; padding : 1px;" src="lib/RSS-ResultsPart.jpg"></p>
+<p class="rvps34"><img alt="" style="width : 654px; height : 298px; padding : 1px;" src="lib/RSS-ResultsPart.jpg"></p>
 <p class="rvps3"><span class="rvts8">After performing the query, the </span><span class="rvts17">Results</span><span class="rvts8"> panel combines all matching experiments into distinct groups sharing the same reaction, sorted by yield. These groups in turn are sorted by their maximum yield item. This provides a result list with the most relevant items first.</span></p>
-<h3 class="rvps32"><span class="rvts0"><span class="rvts45">Explicit substituents</span></span></h3>
+<h3 class="rvps33"><span class="rvts0"><span class="rvts45">Explicit substituents</span></span></h3>
 <p class="rvps3"><span class="rvts8">Please note the explicit hydrogen bonds in above query example:</span></p>
 <p class="rvps10"><img alt="" style="width : 342px; height : 126px; padding : 1px;" src="lib/Explicit_Hydrogens.jpg"></p>
 <p class="rvps3"><span class="rvts8">In substructure queries, explicit substituents are essential for restricting the results to what you want. As a rule, no specified substituent means that any substituent is allowed for a match. In our example, without the explicit hydrogen bonds specified, also e.g. the conversion of a ketone to an ether also would be part of the results. The illustration below explains the role of explicit substituents in more detail (of course, explicit substituents generally are not restricted to hydrogen):</span></p>
 <p class="rvps3"><img alt="" style="width : 362px; height : 239px; padding : 1px;" src="lib/ExplicitBond_Table.jpg"></p>
-<h3 class="rvps32"><span class="rvts0"><span class="rvts45">Local and server search</span></span></h3>
+<h3 class="rvps33"><span class="rvts0"><span class="rvts45">Local and server search</span></span></h3>
 <p class="rvps16"><span class="rvts8">There are two search modes available:</span></p>
 <ul style="text-indent: 0px; padding: 0; margin: 0 0 0 24px; list-style-position: outside; list-style-type: disc;">
  <li class="rvps3 noindent"><span class="rvts29">Local search</span><span class="rvts8">: Searches across your own experiments, no matter if finalized or unfinalized.</span></li>
  <li class="rvps3 noindent"><span class="rvts29">Server search</span><span class="rvts8">: If optionally connected to an in-house ELN server database, this mode searches across all finalized experiments of all users within your organization, including your own ones. Unfinalized experiments, however, are ignored since considered work in progress. Experiment hits of other users can be opened locally and subsequently cloned as an own experiment for repetition or modification.</span></li>
 </ul>
-<h3 class="rvps32"><span class="rvts0"><span class="rvts45">Query Features</span></span></h3>
+<h3 class="rvps33"><span class="rvts0"><span class="rvts45">Query Features</span></span></h3>
 <ul style="text-indent: 0px; padding: 0; margin: 0 0 0 24px; list-style-position: outside; list-style-type: disc;">
  <li class="rvps3 noindent"><span class="rvts8">While explicitly drawn stereochemical centers in a query are recognized, cis/trans geometry is ignored in queries.</span></li>
  <li class="rvps3 noindent"><span class="rvts8">Side products present in experiment reaction sketches currently are ignored. Only reference reactant and reference product are considered.</span></li>

Phoenix ELN Help.hnd-journal

@@ -196,7 +196,7 @@ <h2>Synthetic Connections</h2>
 
 <hr style="height : 1px; background-color : #000000; border-style : none;">
 <p class="rvps18"><span class="rvts15">General</span></p>
-<p class="rvps7"><span class="rvts42">The</span><span class="rvts41"> Synthetic Connections</span><span class="rvts8"> overview identifies and visually maps the entire network of synthetic pathways leading to, and originating from the reaction of the current experiment. In the image below, the step of the current experiment, i.e. the reference step, is marked by a </span><span class="rvts40">➤</span><span class="rvts8"> symbol.</span></p>
+<p class="rvps7"><span class="rvts42">The</span><span class="rvts41"> Synthetic Connections</span><span class="rvts8"> overview identifies and visually maps the entire network of synthetic pathways leading to, and originating from the reaction of the experiment currently displayed in the ELN. In the image below, the step of the current experiment, i.e. the reference step, is marked by a </span><span class="rvts40">➤</span><span class="rvts8"> symbol.</span></p>
 <p class="rvps29"><img alt="" style="width : 643px; height : 448px; padding : 1px;" src="lib/SynthConnDialog.png"><span class="rvts8"> &nbsp; &nbsp; &nbsp;</span></p>
 <p class="rvps30"><span class="rvts8">This overview is accessible from the button located at the bottom right corner of the current reaction sketch:</span></p>
 <p class="rvps30"><span class="rvts8">&nbsp;</span><img alt="" style="width : 227px; height : 92px; padding : 1px;" src="lib/Connections_Button.png"></p>
@@ -207,7 +207,7 @@ <h2>Synthetic Connections</h2>
 <p class="rvps24"><span class="rvts8">The resulting synthetic routes are summarized in a </span><span class="rvts43">flow diagram</span><span class="rvts8"> outlining the sequences of steps leading to and starting from the current experiment (upper section of above image). Each sequence box represents a unique series of synthetic steps. Selecting a specific sequence presents its synthetic step sequence in the lower section of the overview.</span></p>
 <p class="rvps7"><span class="rvts8">The </span><span class="rvts43">step arrows</span><span class="rvts8"> reveal the available highest yield of the experiments the step represents. Clicking a step arrow lists these experiments in the right side panel. The </span><span class="rvts40">➤</span><span class="rvts8"> symbol in front of the step title marks the references step the overview.</span></p>
 <p class="rvps7"><span class="rvts8">Clicking an </span><span class="rvts43">experiment</span><span class="rvts8"> of this list opens it in the background within the ELN. Please note that this does </span><span class="rvts17">not</span><span class="rvts8"> change the current reference step the overview is based on. As mentioned before, when in </span><span class="rvts17">Server Database</span><span class="rvts8"> mode, only </span><span class="rvts30">finalized</span><span class="rvts8"> experiments of users can be accessed, since unfinalized ones are considered work in progress.</span></p>
-<p class="rvps18"><span class="rvts15">Definitions</span></p>
+<p class="rvps32"><span class="rvts15">Definitions</span></p>
 <p class="rvps10"><span class="rvts8">A </span><span class="rvts44">sequence</span><span class="rvts8"> is defined as a </span><span class="rvts17">unique</span><span class="rvts8"> block of subsequent synthetic steps.&nbsp;</span></p>
 <ul style="text-indent: 0px; padding: 0; margin: 0 0 0 24px; list-style-position: outside; list-style-type: disc;">
  <li class="rvps3 noindent"><span class="rvts8">If several sequences share the same final product, they are </span><span class="rvts43">merged</span><span class="rvts8"> either into a downstream sequence, or into a common end product. Merging sequences are assigned an identical sequence number with a suffix </span><span class="rvts17">a, b, c,</span><span class="rvts8"> etc. (i.e. 2a and 2b in our example).&nbsp;</span></li>
@@ -221,7 +221,8 @@ <h2>Synthetic Connections</h2>
  <li class="rvps3 noindent"><span class="rvts8">Clicking the blue </span><span class="rvts17">Reference Step</span><span class="rvts8"> link in the info text at the top of the overview always brings the view back to to this step.</span></li>
  <li class="rvps3 noindent"><span class="rvts8">Step numbers are generated dynamically, based on the experiments currently available for analysis. These step numbers therefore are not suited for use as static references.</span></li>
 </ul>
-<p class="rvps3"><span class="rvts8"><br/></span></p>
+<p class="rvps32"><span class="rvts15">Limitation</span></p>
+<p class="rvps10"><span class="rvts8">The step sequence schemes currently ignore attached component structure properties such as </span><span class="rvts17">rac</span><span class="rvts8">, </span><span class="rvts17">mix</span><span class="rvts8">, </span><span class="rvts17">mon, </span><span class="rvts8">etc., as assigned by component brackets in the drawing tool. Structures with attached properties therefore are treated the same as their underlying structures without these properties.</span></p>
 <p class="rvps3"><span class="rvts8"></span><span class="rvts8"></span></p>
 
             </div>

pages/ReactionSearches.html

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