more english mods

heligeom/templates/about.html

@@ -124,7 +124,7 @@ <h5 class="title_card_results">Screw & Helical Parameters</h5>
           <h5 class="title_card_results">Comparison of interfaces</h5>
           <p>
             If two interfaces are provided, the server provides both sets of helical parameters
-            and additionally computes the <b>Fnat</b> : the fraction of residue-residue contacts shared in the two interfaces,
+            and additionally computes the <b>fNAT</b> : the fraction of residue-residue contacts shared in the two interfaces,
              which is a measure of interface similarity commonly used to evaluate protein-protein docking predictions
              (see <a href="{{ url_for('heligeom_bp.homepage', _anchor='interfaces') }}">the home page</a> for an example.)
           </p>
@@ -145,7 +145,7 @@ <h5 class="title_card_results">Construction of one oligomer</h5>
           <h5 class="title_card_results">Targeted adjustment (i.e Flattening)</h5>
           <p>
             Heligeom can be used to adjust an experimental or a predicted helical assembly having a small pitch and a number of monomers per turn close to an integer value <i>N</i>
-            to attain a ring structure, with zero pitch and precisely <i>N</i> monomers per turn. with a method described in [1].<br>
+            to attain a ring structure, with zero pitch and precisely <i>N</i> monomers per turn, using a method described in [1].<br>
             <br>
             In short, after calculating the screw parameters for two interacting subunits, the adjustment process consists
             in slightly re-positioning and re-orienting the first subunit with respect to the screw axis, which is kept fixed, in such a way that

heligeom/templates/footer.html

@@ -9,8 +9,8 @@
         <div class="col l6 s12">
           <h5>Heligeom version {{version}}</h5>
           <p>
-          The <a href="http://www-lbt.ibpc.fr/">Laboratoire de Biochimie Théorique</a> (LBT, CNRS UPR 9080) is one of five laboratories
-           within the  <a href="http://www.ibpc.fr/">Institut de Biologie Physico-Chimique</a> in Paris.
+		  The <a href="http://www-lbt.ibpc.fr/">Laboratoire de Biochimie Théorique</a> (LBT) is a research laboratory of the French <a href="http://www.cnrs.fr/">National Center for Scientific Research</a> (CNRS) and is one of five laboratories
+		  forming the  <a href="http://www.ibpc.fr/">Institut de Biologie Physico-Chimique</a> (IBPC) in Paris.
           </p>
           <p>
           Our field is theoretical and computational biochemistry, at the interface between biology, chemistry, physics, and computing.

heligeom/templates/help.html

@@ -21,13 +21,13 @@ <h5 class="title_card_results">Examples</h5>
               <li><a href="{{ url_for('heligeom_bp.results', results_id='2GLS') }}">2GLS</a>: an oligomeric ring assembly.
                 By choosing the first two chains (A and B) and constructing an oligomer of 6 elements, you should obtain the first layer of the ring present in the PDB file.<br>
 
-                <li><a href="{{ url_for('heligeom_bp.results', results_id='4ESV_core') }}">4ESV and core regions</a>: This example makes use of Heligeom server's capacity to compare two oligomeric forms to showcase the need for defining a core region in the case of flexible monomers.<br>
-                  For the 1st oligomeric form, the complete chains B and C are specified. In the 2nd oligomeric form, the same chains are studied but a quasi-rigid "core" region is defined that excludes the N-terminal residues.<br>
-                  Heligeom analysis produces different results due to the presence or absence of the N-terminal domain in the analysis. In the first oligomer definition, the large rmsd between the two monomers after superposition reflects the differences in the relative positions of the mobile N-terminal domain. The second oligomeric definition limits the analysis to a more stable core region, which provides a smaller rmsd and better-defined helical parameters.
+                <li><a href="{{ url_for('heligeom_bp.results', results_id='4ESV_core') }}">4ESV and core regions</a>: This example makes use of Heligeom server's capacity to compare two oligomeric forms, here to showcase the need for defining a core region in the case of flexible monomers.<br>
+                  For the 1st oligomeric form, the complete chains B and C are specified. In the 2nd oligomeric form the same two chains are specified, but a quasi-rigid "core" region is defined that excludes the N-terminal residues.<br>
+                  The Heligeom analysis produces different results axccording to the presence or absence of the N-terminal domain in the analysis. In the first oligomer definition, the different relative positions of the mobile N-terminal domain in the two monomers contributes to a large rmsd after superposition. The second oligomeric definition limits the analysis to a less-variable core region, resulting in a smaller rmsd and better-defined helical parameters.
 
                 </li>
-                <li><a href="{{ url_for('heligeom_bp.results', results_id='3ICE_AB_EF') }}">3ICE and alternative interfaces</a>: This example showcases different interfaces within the same structure - here an hexameric ring structure of the Rho transcription termination factor.<br>
-                  Depending of which pairs of chains are chosen for analysis, the fNAT values characterizing the interfaces differ: 0.43 for interface AB vs EF and 0.85 for AB vs BC.
+                <li><a href="{{ url_for('heligeom_bp.results', results_id='3ICE_AB_EF') }}">3ICE and alternative interfaces</a>: This example focuses on different interfaces within the same structure - here an hexameric ring structure of the Rho helicase transcription termination factor.<br>
+                  Depending of which pairs of chains are chosen for analysis, the fNAT values characterizing the interfaces differ: here 0.43 for interface AB vs EF and 0.85 for AB vs BC.
                 </li>
             </ul>
 
@@ -44,7 +44,7 @@ <h5 class="header">1 - First Oligomeric form</h5>
             <img class="responsive-img" src="{{ url_for('static', filename='img/run_1.png')}}"style="max-width:80%;">
           </div>
           <p>
-            The form is organised in two parts: the <span style="color: #4472c4">Input data</span>
+            The input form is organised in two parts: the <span style="color: #4472c4">Input data</span>
             and the <span style="color: #ed7d31">Selection</span>. <br />
             <br />
             In the <span style="color: #4472c4">Input data</span>, you can either:
@@ -55,7 +55,7 @@ <h5 class="header">1 - First Oligomeric form</h5>
             From this input PDB, in the <span style="color: #ed7d31">Selection</span> section, you'll need to define the two monomers for which the interface and the Screw parameters will be computed.<br />
             <b>Note: A <i>cleaning</i> step is performed in which all HETATM and water atoms are discarded from the input PDB.</b><br />
             For each monomer you can specify the chain, the residue range, or both.<br />
-            <b><i class="tiny material-icons valign">priority_high</i>Only the α-carbon of the monomers will be used for computing the helical parameters. Both monomers needs to have the same number.</b><i class="tiny material-icons valign">priority_high</i>
+            <b><i class="tiny material-icons valign">priority_high</i>Only the α-Carbon of the monomers will be used for computing the helical parameters. Both monomers needs to have the same number.</b><i class="tiny material-icons valign">priority_high</i>
           </p>
           <p>
             <b>Core Region:</b> A core region is a specific region of the monomer which will be used to compute the helical parameters and the residues at the interface.<br>
@@ -87,7 +87,7 @@ <h5 class="header">2 - 2nd Oligomeric form (Optional)</h5>
 
           <p>
             Helligeom allows you also to compare 2 interfaces by specifying a second interface.<br />
-            To do so, you must click on the text <i>2nd oligomeric form?</i>, and a new form as for the first oligomeric form will appear.
+            To do so, you must click on the text <i>2nd oligomeric form?</i>, and a new input form as for the first oligomeric form will appear.
           </p>
 
           <div class="center-align img_help">
@@ -186,7 +186,7 @@ <h5 class="header">Construction Details</h5>
             <ul class="browser-default">
              <li>take the entire Monomer 1 selection (not just the <i>core regions</i>), including non-protein atoms if they are part of the selection.</li>
              <li>create copies of this monomer applying the screw transformation</li>
-             <li>repeat the above step to match the number of monomers given by the form.</li>
+             <li>repeat the above step to match the number of monomers provided as input.</li>
             </ul>
             <b>Alignment on Z-axis?: </b>This option enables the alignment the oligomer to the global Z-axis.<br />
             <b>Write a mmCIF file?: </b>This option writes the structure file for the oligomer using the mmCIF file format instead of the PDB flat-file format. This is useful when constructing assemblies with more than 62 chains.<br />
@@ -200,7 +200,7 @@ <h6 id="flatten"><b>Flatten the oligomer?</b></h6>
           </p>
           <br >
           <br >
-          Once the construction is finished, an interactive view of the oligomer is displayed below the form (thanks to <a href="https://molstar.org/">Mol*</a>).
+          Once the construction is finished, an interactive view of the oligomer is displayed below the input form (thanks to <a href="https://molstar.org/">Mol*</a>).
           <div class="center-align img_help">
             <img class="responsive-img" src="{{ url_for('static', filename='img/result_1_bot_visu.png')}}"style="max-width:80%;">
           </div>

heligeom/templates/index.html

@@ -11,7 +11,7 @@
         <h2 class="header center orange-text text-darken-2">Welcome to Heligeom Webserver</h2>
         <div class="row center">
           <h5 class="header col s12 lbt-dark-grey-text">
-            Relating interfaces to 3D architectures
+            Relating interfaces to supramolecular architectures
           </h5>
         </div>
   </div>
@@ -56,8 +56,6 @@ <h5 class="header lbt-grey-text" id="screw">Screw organization</h5>
       number of monomers per turn and the handedness. A cyclic oligomer, or ring, is a special case of a screw
       assembly in which the pitch is null. The linear (straight) assembly is another special case
 	  in which the rotation around the axis is null.<br>
-      (However, while the interface geometry between subunits defines the 3D organization and thus the pitch and
-      number of monomers per turn, these two parameters alone are not sufficient to specify the helical geometry.)<br>
     </p>
 
     <div class="center-align">
@@ -67,7 +65,7 @@ <h5 class="header lbt-grey-text" id="screw">Screw organization</h5>
       <h5 class="header lbt-grey-text" id="interfaces">Interfaces</h5>
 
       <p>
-        A binding geometry can be characterized by a set of pairs of amino-acid in contact across the
+        A binding geometry may be characterized by a set of pairs of amino-acid in contact across the
         interface. Thus different oligomers may be considered to be members of the same family if they
         share a sufficient fraction of contact pairs. <br>
         This ratio is called f<sub>NAT</sub> (fraction of NATive contacts) due to its historical definition

heligeom/templates/macros/results.html

@@ -108,7 +108,7 @@ <h6 style="color:#F57C00">Monomer 2</h6>
 {%- endmacro %}
 
 {% macro display_rmsd(data) -%}
-<div class="center tooltipped" data-position="top" data-tooltip="RMSD is computed between the Carbon-α of the 2 monomers." style="margin-top: 20px;">
+<div class="center tooltipped" data-position="top" data-tooltip="RMSD is computed between the α-Carbons of the 2 monomers." style="margin-top: 20px;">
   {% if (data.rmsd | float < 2) %}
     <div class="green-text text-darken-3">
       RMSD: <b>{{ data.rmsd }}</b>  <i class="valign tiny material-icons">help</i>

heligeom/templates/partial/loading.html

@@ -5,7 +5,7 @@
     </div>
   </div>
   <div class="row">
-    <h2 class="header light blue-grey-text text-darken-3 center-align">Analyze in process...</h2>
+    <h2 class="header light blue-grey-text text-darken-3 center-align">Analysis in process...</h2>
   </div>
 </div> <!-- end section -->
 

heligeom/templates/run.html

@@ -43,7 +43,7 @@ <h2 class="header center orange-text text-darken-2">Run Heligeom</h2>
                   <p>For each monomer, you can specify the <b>chain of interest</b> or the <b>residue range</b>, or <b>both</b>.</p>
                   <p><b>Note:</b> This tool can handle missing residues within the selection (to manage flexible/unstructured sections).</p>
                     <p>In this case, The 2 monomers <b>must</b> have a residue range of the same length (e.g., <i>1-300</i> and <i>301-600</i>).</p>
-                    <p class="red-text light"><b>Please make sure that both selected monomers (with or without core regions) have the same number of α carbons.</b></p>
+                    <p class="red-text light"><b>Please make sure that both selected monomers (with or without core regions) have the same number of α-Carbons.</b></p>
                   <br>
                   <div class="col s12 m6">
                     {{ forms_macro.monomer_card(1, form.chain1_id, form.res_range1, form.core_filter1, form.core_region1) }}
@@ -72,7 +72,7 @@ <h2 class="header center orange-text text-darken-2">Run Heligeom</h2>
                         <p>For each monomer, you can specify the <b>chain of interest</b> or the <b>residue range</b>, or <b>both</b>.</p>
                         <p><b>Note:</b> This tool can handle missing residues within the selection (to manage flexible/unstructured sections).</p>
                           <p>In this case, The 2 monomers <b>must</b> have a residue range of the same length (e.g., <i>1-300</i> and <i>301-600</i>).</p>
-                          <p class="red-text light"><b>Please make sure that both selected monomers (with or without core regions) have the same number of α carbons.</b></p>
+                          <p class="red-text light"><b>Please make sure that both selected monomers (with or without core regions) have the same number of α-Carbons.</b></p>
                         <br>
                           <div class="col s12 m6">
                             {{ forms_macro.monomer_card("1 bis", form.chain1bis_id, form.res_range1bis, form.core_filter1bis, form.core_region1bis) }}