Pull request #650: Draw coils for the whole structure with zero radiu…

…s for the secondary structure parts.

Merge in STRUC/icn3d from release3331 to master

* commit '8e7f7c7eabbdaa51019e98b4777bb05d11eda00e':
  Draw coils for the whole structure with zero radius for the secondary structure parts.
  Draw coils for the whole structure with zero radius for the secondary structure parts.

CHANGELOG.md

@@ -1,4 +1,6 @@
 ## Change Log
+[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. 
+
 [icn3d-3.33.0](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-3.33.0.zip) was release on June 12, 2024. Users can use iCn3D to detect Ig domains for any structures and assign IgStrand reference numbers for each residue. The instruction is at https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d.html#igrefnum.  
 
 [icn3d-3.32.0](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-3.32.0.zip) was release on May 28, 2024. Allowed to load multiple mmCIF text files, which could contain multiple structures separated by "ENDMDL\n". 

dist/CHANGELOG.md

@@ -1,4 +1,6 @@
 ## Change Log
+[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. 
+
 [icn3d-3.33.0](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-3.33.0.zip) was release on June 12, 2024. Users can use iCn3D to detect Ig domains for any structures and assign IgStrand reference numbers for each residue. The instruction is at https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d.html#igrefnum.  
 
 [icn3d-3.32.0](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-3.32.0.zip) was release on May 28, 2024. Allowed to load multiple mmCIF text files, which could contain multiple structures separated by "ENDMDL\n". 

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_3.33.0.css">
+  <link rel="stylesheet" href="icn3d_3.33.1.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_3.33.0.min.js"></script>
+  <script src="icn3d_3.33.1.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 {
-          //$.getScript('icn3d_3.33.0.min.js', function() {
+          //$.getScript('icn3d_3.33.1.min.js', function() {
             var version = 3;
             await launchIcn3d(version); //await 
           //});

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_3.33.0.css">
+  <link rel="stylesheet" href="icn3d_3.33.1.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_3.33.0.min.js"></script>
+  <script src="icn3d_3.33.1.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_3.33.0.min.js', function() {
+          //$.getScript('icn3d_3.33.1.min.js', function() {
             var version = 3;
             await launchIcn3d(version);
           //});

dist/full2_3.33.0.html → dist/full2_3.33.1.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_3.33.0.css">
+  <link rel="stylesheet" href="icn3d_3.33.1.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_3.33.0.min.js"></script>
+  <script src="icn3d_3.33.1.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_3.33.0.min.js', function() {
+          //$.getScript('icn3d_3.33.1.min.js', function() {
             var version = 3;
             await launchIcn3d(version);
           //});

dist/full_3.33.0.html → dist/full_3.33.1.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_3.33.0.css">
+  <link rel="stylesheet" href="icn3d_3.33.1.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_3.33.0.min.js"></script>
+  <script src="icn3d_3.33.1.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 {
-          //$.getScript('icn3d_3.33.0.min.js', function() {
+          //$.getScript('icn3d_3.33.1.min.js', function() {
             var version = 3;
             await launchIcn3d(version); //await 
           //});

dist/icn3d.html

@@ -898,7 +898,7 @@ <h3>Frequently Asked Questions<img src="https://www.ncbi.nlm.nih.gov/Structure/I
 <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>
     <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.<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>
 </li>
 
@@ -2793,7 +2793,7 @@ <h3>Class Structure<img src="https://www.ncbi.nlm.nih.gov/Structure/IMG/spacer.g
 <tr><td>icn3d</td><td>icn3dui</td><td>icn3d</td><td>residueLabelsCls (geometry)</td><td>addResidueLabels, addNonCarbonAtomLabels, addAtomLabels</td></tr>
 <tr><td>icn3d</td><td>icn3dui</td><td>icn3d</td><td>sphereCls (geometry)</td><td>createSphere, createSphereBase, createSphereRepresentation</td></tr>
 <tr><td>icn3d</td><td>icn3dui</td><td>icn3d</td><td>stickCls (geometry)</td><td>createStickRepresentation</td></tr>
-<tr><td>icn3d</td><td>icn3dui</td><td>icn3d</td><td>strandCls (geometry)</td><td>createStrand, getSSExpandedAtoms</td></tr>
+<tr><td>icn3d</td><td>icn3dui</td><td>icn3d</td><td>strandCls (geometry)</td><td>createStrand, getOneExtraResidue</td></tr>
 <tr><td>icn3d</td><td>icn3dui</td><td>icn3d</td><td>stripCls (geometry)</td><td>createStrip, setCalphaDrawnCoord</td></tr>
 <tr><td>icn3d</td><td>icn3dui</td><td>icn3d</td><td>tubeCls (geometry)</td><td>createTube, getCustomtubesize, createTubeSub, getRadius</td></tr>