minor language and hyperlink updates

salilab · Mar 28, 2024 · 4c0fd30 · 4c0fd30
1 parent 3cc815b
commit 4c0fd30
Show file tree

Hide file tree

Showing 3 changed files with 10 additions and 6 deletions.
diff --git a/templates/cx_data_quality.j2 b/templates/cx_data_quality.j2
@@ -9,14 +9,18 @@
             <u><a name=crosslinking-ms>Crosslinking-MS</a></u>
           </h5>
           <p align=justify>
-            <em>At the moment, data validation is only available for crosslinking-MS datasets deposited in a standardized mzIdentML format to PRIDE</em>.
+            <em>
+              At the moment, data validation is only available for crosslinking-MS datasets deposited in a standardized <mzIdentML format to <a href=https://www.ebi.ac.uk/pride/archive/crosslinking>PRIDE</a> database. 
+              Correspondence between crosslinking-MS and entry entities is established using <a href=https://pyhmmer.readthedocs.io/en/stable/>pyHMMER</a>. Only residue pairs that passed the reported threshold are used for the analysis. The values in the report have to be interpreted in the context
+              of the experiment (i.e. only a minor fraction of in-situ or in-vivo dataset can be used for modeling).
+            </em>
           </p>
           {% if cx_data_quality|length > 0 %}
             {% for data in cx_data_quality %}
               <div name=crosslinking-ms-{{ data["pride_id"] }} {{ 'class="card-header" style="background-color: #FFF;"' if cx_data_quality|length > 1 }}>
                 <table vertical-align: middle;">
                   <tr>
-                    <td>Crosslinking-MS dataset (<a href=https://www.ebi.ac.uk/pride/>PRIDE ID</a>)</td>
+                    <td>Crosslinking-MS dataset (<a href=https://www.ebi.ac.uk/pride/archive/crosslinking>PRIDE ID</a>)</td>
                     <td><a href=https://www.ebi.ac.uk/pride/archive/crosslinking/{{ data["pride_id"] }}>{{ data["pride_id"] }}</a></td>
                   </tr>
                   <tr>

diff --git a/templates/formodeling.html b/templates/formodeling.html
@@ -154,8 +154,8 @@ <h5 align=center id="crosslinking-ms_satisfaction"><u>Satisfaction of restraints
                 <div class=col-lg-6>
                   <p>
                     <i>
-                      Satisfaction of restraints is calculated on a restraint 
-                      group level. Satisfaction of a restraint group depends on 
+                      Satisfaction of restraints is calculated on a <a href=https://mmcif.wwpdb.org/dictionaries/mmcif_ihm_ext.dic/Categories/ihm_cross_link_restraint.html>restraint 
+                        group level</a>. Satisfaction of a restraint group depends on 
                       satisfaction of individual restraints in the group and the 
                       conditionality (all/any). Restraint group is considered 
                       satisfied, if condition was met in at least one model of 

diff --git a/templates/full_validation_pdf.html b/templates/full_validation_pdf.html
@@ -843,8 +843,8 @@ <h5 align=center id="cxms_satisfaction">
                   <div class=col-lg-12>
                     <p>
                       <i>
-                        Satisfaction of restraints is calculated on a restraint 
-                        group level. Satisfaction of a restraint group depends on 
+                        Satisfaction of restraints is calculated on a <a href=https://mmcif.wwpdb.org/dictionaries/mmcif_ihm_ext.dic/Categories/ihm_cross_link_restraint.html>restraint 
+                        group level</a>. Satisfaction of a restraint group depends on 
                         satisfaction of individual restraints in the group and the 
                         conditionality (all/any). Restraint group is considered 
                         satisfied, if condition was met in at least one model of