Pull request #654: Switch electron density data from RCSB DSN6 to PDB…

…e Density Server. Merge in STRUC/icn3d from release3333 to master * commit 'fbd88daadb6ccd10603f8ec55259e9bb4ffe8dd1': Switch electron density data from RCSB DSN6 to PDBe Density Server.
ncbi · Jul 15, 2024 · 29768e5 · 29768e5
2 parents c8f233d + fbd88da
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,7 @@
 ## Change Log
-[icn3d-3.33.2](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-3.33.1.zip) was release on June 25, 2024. Enabled to measure angles between sets in the menu "Analysis > Angle". 
+[icn3d-3.33.3](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-3.33.3.zip) was release on July 15, 2024. Switch electron density data from RCSB DSN6 to PDBe Density Server. 
+
+[icn3d-3.33.2](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-3.33.2.zip) was release on June 25, 2024. Enabled to measure angles between sets in the menu "Analysis > Angle". 
 
 [icn3d-3.33.1](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-3.33.1.zip) was release on June 18, 2024. Draw coils for the whole structure with zero radius for the secondary structure parts. 
 

diff --git a/LICENSE.md b/LICENSE.md
diff --git a/README.md b/README.md
diff --git a/SECURITY.md b/SECURITY.md
diff --git a/build/icn3d.js b/build/icn3d.js
diff --git a/build/icn3d.min.js b/build/icn3d.min.js
diff --git a/build/icn3d.module.js b/build/icn3d.module.js
diff --git a/dist/CHANGELOG.md b/dist/CHANGELOG.md
@@ -1,5 +1,7 @@
 ## Change Log
-[icn3d-3.33.2](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-3.33.1.zip) was release on June 25, 2024. Enabled to measure angles between sets in the menu "Analysis > Angle". 
+[icn3d-3.33.3](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-3.33.3.zip) was release on July 15, 2024. Switch electron density data from RCSB DSN6 to PDBe Density Server. 
+
+[icn3d-3.33.2](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-3.33.2.zip) was release on June 25, 2024. Enabled to measure angles between sets in the menu "Analysis > Angle". 
 
 [icn3d-3.33.1](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-3.33.1.zip) was release on June 18, 2024. Draw coils for the whole structure with zero radius for the secondary structure parts. 
 

diff --git a/dist/full.html b/dist/full.html
@@ -19,11 +19,11 @@
   <div id="div0"></div>
 
   <link rel="stylesheet" href="lib/jquery-ui-1.13.2.min.css">
-  <link rel="stylesheet" href="icn3d_3.33.2.css">
+  <link rel="stylesheet" href="icn3d_3.33.3.css">
   <script src="lib/jquery-3.5.0.min.js"></script>
   <script src="lib/jquery-ui-1.13.2.min.js"></script>
   <script src="lib/three_0.151.0.min.js"></script>
-  <script src="icn3d_3.33.2.min.js"></script>
+  <script src="icn3d_3.33.3.min.js"></script>
 
   <script type="text/javascript">
 
@@ -41,7 +41,7 @@
           alert("IE does NOT work with the current iCn3D version 3. The old iCn3D version 2 is used instead.");
       }
       else {
-          //$.getScript('icn3d_3.33.2.min.js', function() {
+          //$.getScript('icn3d_3.33.3.min.js', function() {
             var version = 3;
             await launchIcn3d(version); //await 
           //});

diff --git a/dist/full2.html b/dist/full2.html
@@ -20,11 +20,11 @@
   <div id="div1" style="float:left;"></div>
 
   <link rel="stylesheet" href="lib/jquery-ui-1.13.2.min.css">
-  <link rel="stylesheet" href="icn3d_3.33.2.css">
+  <link rel="stylesheet" href="icn3d_3.33.3.css">
   <script src="lib/jquery-3.5.0.min.js"></script>
   <script src="lib/jquery-ui-1.13.2.min.js"></script>
   <script src="lib/three_0.151.0.min.js"></script>
-  <script src="icn3d_3.33.2.min.js"></script>
+  <script src="icn3d_3.33.3.min.js"></script>
 
   <script type="text/javascript">
     $( document ).ready(async function() {
@@ -41,7 +41,7 @@
           alert("IE does NOT work with the current iCn3D version 3. The old iCn3D version 2 is used instead.");
       }
       else {
-          //$.getScript('icn3d_3.33.2.min.js', function() {
+          //$.getScript('icn3d_3.33.3.min.js', function() {
             var version = 3;
             await launchIcn3d(version);
           //});

diff --git a/dist/full2_3.33.2.html → dist/full2_3.33.3.html b/dist/full2_3.33.2.html → dist/full2_3.33.3.html
@@ -20,11 +20,11 @@
   <div id="div1" style="float:left;"></div>
 
   <link rel="stylesheet" href="lib/jquery-ui-1.13.2.min.css">
-  <link rel="stylesheet" href="icn3d_3.33.2.css">
+  <link rel="stylesheet" href="icn3d_3.33.3.css">
   <script src="lib/jquery-3.5.0.min.js"></script>
   <script src="lib/jquery-ui-1.13.2.min.js"></script>
   <script src="lib/three_0.151.0.min.js"></script>
-  <script src="icn3d_3.33.2.min.js"></script>
+  <script src="icn3d_3.33.3.min.js"></script>
 
   <script type="text/javascript">
     $( document ).ready(async function() {
@@ -41,7 +41,7 @@
           alert("IE does NOT work with the current iCn3D version 3. The old iCn3D version 2 is used instead.");
       }
       else {
-          //$.getScript('icn3d_3.33.2.min.js', function() {
+          //$.getScript('icn3d_3.33.3.min.js', function() {
             var version = 3;
             await launchIcn3d(version);
           //});

diff --git a/dist/full_3.33.2.html → dist/full_3.33.3.html b/dist/full_3.33.2.html → dist/full_3.33.3.html
@@ -19,11 +19,11 @@
   <div id="div0"></div>
 
   <link rel="stylesheet" href="lib/jquery-ui-1.13.2.min.css">
-  <link rel="stylesheet" href="icn3d_3.33.2.css">
+  <link rel="stylesheet" href="icn3d_3.33.3.css">
   <script src="lib/jquery-3.5.0.min.js"></script>
   <script src="lib/jquery-ui-1.13.2.min.js"></script>
   <script src="lib/three_0.151.0.min.js"></script>
-  <script src="icn3d_3.33.2.min.js"></script>
+  <script src="icn3d_3.33.3.min.js"></script>
 
   <script type="text/javascript">
 
@@ -41,7 +41,7 @@
           alert("IE does NOT work with the current iCn3D version 3. The old iCn3D version 2 is used instead.");
       }
       else {
-          //$.getScript('icn3d_3.33.2.min.js', function() {
+          //$.getScript('icn3d_3.33.3.min.js', function() {
             var version = 3;
             await launchIcn3d(version); //await 
           //});

diff --git a/dist/icn3d-3.33.2.zip → dist/icn3d-3.33.3.zip b/dist/icn3d-3.33.2.zip → dist/icn3d-3.33.3.zip
diff --git a/dist/icn3d.html b/dist/icn3d.html
@@ -896,7 +896,11 @@ <h3>Frequently Asked Questions<img src="https://www.ncbi.nlm.nih.gov/Structure/I
 </li>
 
 <li><span class="anchor" id="igrefnum"></span><a name="igrefnum"></a><b>Q: How to use iCn3D to assign Ig reference numbers?</b><br>
-    You can assign IgStrand reference numbers via the menu "Analysis > Ref. Number > Show Ig for Selection", or via the menu "Analysis > Seq. & Annotations" and click the checkbox "Ig Domains" in the "Annotations" section. The reference numbers can be exported via the menu "File > Save File > Reference Numbers". See the manuscript <a href="https://www.biorxiv.org/content/10.1101/2024.06.10.598201v1">A universal residue numbering scheme for the Immunoglobulin-fold (Ig-fold) to study Ig-Proteomes and Ig-Interactomes</a> for more details.<br>
+    iCn3D provides an automatic way to detect Ig domains and assign "IgStrand" reference numbers for all residues so that users can cross-compare residues in different Ig domains using the reference numbers.<br>
+    <br>
+    A list of about 55 Ig templates are used to align the input structure using TM-align. The template with the highest TM-score is selected as the template to assign the reference numbers for each strand in the Ig domain. Different from Kabat and IMGT reference numbers for Ig domains, "IgStrand" reference numbers are similar to GPCR reference numbers. An anchor residue in each strand is assigned a 4-digit number ##50. For example, the refernce number 1550 is the anchor residue for "A" strand. The residues before and after the anchor residue are assigned as continuous numbers: ##48, ##49, and ##51, ##52, respectively. Each strand has a predefined color so that users can easily tell the strands from the color. See the manuscript <a href="https://www.biorxiv.org/content/10.1101/2024.06.10.598201v1">A universal residue numbering scheme for the Immunoglobulin-fold (Ig-fold) to study Ig-Proteomes and Ig-Interactomes</a> for more details.<br>
+    <br>
+    You can assign IgStrand reference numbers via the menu "Analysis > Ref. Number > Show Ig for Selection", or via the menu "Analysis > Seq. & Annotations" and click the checkbox "Ig Domains" in the "Annotations" section. The reference numbers can be exported via the menu "File > Save File > Reference Numbers".<br>
     <br>
     If you want to process a list of structures, you can download iCn3D Node.js script "refnum.js" at https://github.com/ncbi/icn3d/tree/master/icn3dnode. This script runs TM-align locally using the program at https://github.com/ncbi/icn3d/tree/master/icn3dnode/tmalign-icn3dnode and the templates at https://github.com/ncbi/icn3d/tree/master/icn3dnode/refpdb. One example is listed at the section “Detect Ig domains and assign IgStrand reference numbers” at https://github.com/ncbi/icn3d/tree/master/icn3dnode.<br>
     <br>