Merge pull request #21 in STRUC/icn3d from release101 to master

* commit '14c1f92ef047967bc172bca6970184651f9e4f43':
  fixed the version of three.js
  fixed version number and changed some buttons

README.md

@@ -11,7 +11,7 @@ We provided two versions of iCn3D widgets: [basic interface](https://www.ncbi.nl
 
 Either of these widgets could be easily added to your own web pages. Please see the [help page](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d.html) for more details.
 
-<b>Complete package</b> of iCn3D including Three.js and jQuery can be downloaded from [https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-1.0.zip](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-1.0.zip). The "Download ZIP" link in this page does not include these third-party libraries. 
+<b>Complete package</b> of iCn3D including Three.js and jQuery can be downloaded from [https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-1.0.1.zip](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-1.0.1.zip). The "Download ZIP" link in this page does not include these third-party libraries. 
 
 ## Usage
 
@@ -86,21 +86,7 @@ gulp gh-pages
 
 ## Change log
 
-The beta version [icn3d-0.9.0-dev](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-0.9.0-dev.zip) was release on Jan 17, 2016. 
-
-The beta version [icn3d-0.9.1-dev](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-0.9.1-dev.zip) was release on Feb 9, 2016. The surface generation was switched from the iview version (surface.js) to the more efficient 3Dmol version (ProteinSurface4.js and marchingcube.js).
-
-The beta version [icn3d-0.9.2-dev](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-0.9.2-dev.zip) was release on March 4, 2016. CSS namespace was added. The file simple_ui.js was reorganized to share some codes with full_ui.js. A "Schematic" style was added to show one letter residue name in the C-alpha (for protein) or phosphorus (for nucleotide) position.
-
-The beta version [icn3d-0.9.3-dev](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-0.9.3-dev.zip) was release on March 9, 2016. Improved the following features: "Back" and "Forward" button, Export State, Open State.
-
-The beta version [icn3d-0.9.4-dev](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-0.9.4-dev.zip) was release on March 14, 2016. Added "Fog" and "Slab" features.
-
-The beta version [icn3d-0.9.5-dev](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-0.9.5-dev.zip) was release on April 4, 2016. Enabled to import Mol2, SDF, XYZ, PDB, and mmCIF files. Added "Schematic" style for ligands. Improved the coordination between picking on 3D structure and selection on sequences.
-
-The beta version [icn3d-0.9.6-dev](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-0.9.6-dev.zip) was release on April 21, 2016. Enabled to export and import selection file where each custom sets of atoms are defined. Javascript files and CSS files are versioned. Developers can use the default latest version or specify the specific version in their pages.
-
-The production version [icn3d-1.0](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-1.0.zip) was release on April 28, 2016. 
+The production version [icn3d-1.0.1](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-1.0.1.zip) was release on May 16, 2016. All previous releases can be found at the [help page](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d.html#log).
 
 ## Contact
 

gulpfile.js

@@ -27,7 +27,7 @@ gulp.task('libs',
             "node_modules/jquery/dist/jquery.min.js",
             "node_modules/jquery-ui/jquery-ui.min.js",
             "node_modules/three/three.min.js",
-            "node_modules/three/three_v71.min.js",
+            "node_modules/three/three_0.71.1.min.js",
         ])
         .pipe(gulp.dest(dist + '/lib'));
   });

icn3d.html

@@ -101,11 +101,15 @@ <h2>What is iCn3D Structure Viewer?<img src="https://www.ncbi.nlm.nih.gov/Struct
         <li><a href="#HowToUseStep1">Include three.js and jQuery javascript libraries in the &lt;head&gt; of your html page</a></li>
         <li><a href="#HowToUseStep2">Position the widget with an html div</a></li>
         <li><a href="#HowToUseStep3">Initialize the widget with desired parameters</a></li>
+        </ol>
+    </li>
+    <li><a href="#hints">Hints for using iCn3D</a><br>
+        <ul>
         <li><a href="#HowToUseStep4">Hint for rotating/translating/zooming the 3D structure</a></li>
         <li><a href="#HowToUseStep5">Hint for picking 3D structure and selecting sequences</a></li>
         <li><a href="#HowToUseStep6">Hint for recovering a crashed page</a></li>
         <li><a href="#HowToUseStep7">Hint for turning on scroll bars in Mac</a></li>
-        </ol>
+        </ul>
     </li>
     </ul>
 <br>
@@ -365,6 +369,8 @@ <h2>What is iCn3D Structure Viewer?<img src="https://www.ncbi.nlm.nih.gov/Struct
 </tr>
 </tbody></table>
 
+<li><a href="#log">Change Log</a></li>
+
 </ul>
 
 <hr>
@@ -456,7 +462,10 @@ <h2>How to use iCn3D Structure Viewer in your html page:<img src="https://www.nc
   &lt;/script&gt;</pre>
     </li>
     </ul>
+</ol>
 
+<li><a name="hints"></a><b>Hints for using iCn3D</b><br>
+  <ul>
     <li><a name="HowToUseStep4"></a><b>Hint for rotating/translating/zooming the 3D structure:</b></li>
     <ul>
       <li>Rotate
@@ -503,7 +512,7 @@ <h2>How to use iCn3D Structure Viewer in your html page:<img src="https://www.nc
     <div>If you are using Macintosh computer and need to scroll in the sequence dialog, you can turn on the scroll bars as follows: Systems preferences -> GENERAL -> show scroll bars -> check "always".
     </div>
 
-</ol>
+</ul>
 </li>
 </ul>
 
@@ -529,7 +538,7 @@ <h2>URL parameters for the advanced interface<img src="https://www.ncbi.nlm.nih.
 <tr valign='top'><td>showmenu</td><td>No</td><td>Yes</td><td>Set "true" or "1" to show the menus and buttons at the top of the structure canvas. The default is "true".</td></tr>
 <tr valign='top'><td>showseq</td><td>No</td><td>Yes</td><td>Set "true" or "1" to show the sequence window. The default is "false".</td></tr>
 <tr valign='top'><td>showalignseq</td><td>No</td><td>Yes</td><td>Set "true" or "1" to show the aligned sequence window. The default is "false".</td></tr>
-<tr valign='top'><td><a name="commandsUrl"></a>command</td><td>No</td><td>Yes</td><td>Besides the "Script/Log" section, commands can also be attached to the url parameter "command". Several commands can be concatenated with the separator ";", e.g., <a href="full.html?mmdbid=1kq2&amp;command=select :1-20; color green">full.html?mmdbid=1kq2&amp;command=select :1-20; color green</a>.</td></tr>
+<tr valign='top'><td><a name="commandsUrl"></a>command</td><td>No</td><td>Yes</td><td>Besides the "Script/Log" section, commands can also be attached to the url parameter "command". Several commands can be concatenated with the separator ";", e.g., <a href="full.html?mmdbid=3gvu&command=select .A:38-40 or .A:42 or .A:45 or .A:61 or .A:63 or .A:77-78 or .A:82 or .A:91 or .A:107-108 or .A:110 or .A:114 or .A:162 or .A:172-173; style proteins stick; color atom; set surface Van der Waals surface; add label ATP-binding Site | size 18 | color #0000ff | background #cccccc | type custom; select .STI; color green; toggle highlight">full.html?mmdbid=3gvu&amp;command=select .A:38-40 or .A:42 or .A:45 or .A:61 or .A:63 or .A:77-78 or .A:82 or .A:91 or .A:107-108 or .A:110 or .A:114 or .A:162 or .A:172-173; style proteins stick; color atom; set surface Van der Waals surface; add label ATP-binding Site | size 18 | color #0000ff | background #cccccc | type custom; select .STI; color green; toggle highlight</a>.</td></tr>
 </table>
 
 <hr>
@@ -1466,8 +1475,43 @@ <h2>API Documents of the advanced UI library iCn3DUI<img src="https://www.ncbi.n
 
 
 
-<br>
+<br><br>
+
+<hr>
+
+<a name="log"></a>
+<h2>Change Log:<img src="https://www.ncbi.nlm.nih.gov/Structure/IMG/spacer.gif" width="25" height="1" border="0"><a href="#Top"><img src="https://www.ncbi.nlm.nih.gov/Structure/IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></a></h2>
 
+The production version <a href="https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-1.0.0.zip">icn3d-1.0.1</a> was release on May 16, 2016.
+<br><br>
+
+The production version <a href="https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-1.0.0.zip">icn3d-1.0.0</a> was release on April 28, 2016.
+<br><br>
+
+The beta version <a href="https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-0.9.6-dev.zip">icn3d-0.9.6-dev</a> was release on April 21, 2016. Enabled to export and import selection file where each custom sets of atoms are defined. Javascript files and CSS files are versioned. Developers can use the default latest version or specify the specific version in their pages.
+<br><br>
+
+The beta version <a href="https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-0.9.5-dev.zip">icn3d-0.9.5-dev</a> was release on April 4, 2016. Enabled to import Mol2, SDF, XYZ, PDB, and mmCIF files. Added "Schematic" style for ligands. Improved the coordination between picking on 3D structure and selection on sequences.
+<br><br>
+
+The beta version <a href="https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-0.9.4-dev.zip">icn3d-0.9.4-dev</a> was release on March 14, 2016. Added "Fog" and "Slab" features.
+<br><br>
+
+The beta version <a href="https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-0.9.3-dev.zip">icn3d-0.9.3-dev</a> was release on March 9, 2016. Improved the following features: "Back" and "Forward" button, Export State, Open State.
+<br><br>
+
+The beta version <a href="https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-0.9.2-dev.zip">icn3d-0.9.2-dev</a> was release on March 4, 2016. CSS namespace was added. The file simple_ui.js was reorganized to share some codes with full_ui.js. A "Schematic" style was added to show one letter residue name in the C-alpha (for protein) or phosphorus (for nucleotide) position.
+<br><br>
+
+The beta version <a href="https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-0.9.2-dev.zip">icn3d-0.9.2-dev</a> was release on March 4, 2016. CSS namespace was added. The file simple_ui.js was reorganized to share some codes with full_ui.js. A "Schematic" style was added to show one letter residue name in the C-alpha (for protein) or phosphorus (for nucleotide) position.
+<br><br>
+
+The beta version <a href="https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-0.9.1-dev.zip">icn3d-0.9.1-dev</a> was release on Feb 9, 2016. The surface generation was switched from the iview version (surface.js) to the more efficient 3Dmol version (ProteinSurface4.js and marchingcube.js).
+<br><br>
+
+The beta version <a href="https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-0.9.0-dev.zip">icn3d-0.9.0-dev</a> was release on Jan 17, 2016.
+
+<br>
 
 <!-- ======================= END_EXAMPLES ======================= -->
 

package.json

@@ -1,6 +1,6 @@
 {
   "name": "icn3d",
-  "version": "1.0.0",
+  "version": "1.0.1",
   "description": "iCn3D Structure Viewer",
   "main": "index.html",
   "scripts": {