<head><title>Popup Menu</title></head>\r
\r
<body>\r
-<p><strong>Popup Menu</strong></p>\r
-<p><em>Define </em></p>\r
+<p><strong>Popup Menu</strong><br>\r
+ <em>This menu is visible when right clicking either within a selected region \r
+ on the alignment or on a selected sequence name.</em></p>\r
<ul>\r
- <li>Group, </li>\r
- <li>Remove Group</li>\r
- <li>Group Colour</li>\r
- <li>Boxes</li>\r
- <li> Text</li>\r
- <li>Colour Text</li>\r
- <li>Border Colour </li>\r
-</ul>\r
-<p><em>Sequence</em> </p>\r
-<ul>\r
- <li>Edit Name</li>\r
- <li>View PDB Structure</li>\r
+ <li><strong>Define </strong> \r
+ <ul>\r
+ <li><strong>Group<br>\r
+ </strong><em>This will display a window asking for the name of the currently \r
+ selected group. Click OK to set the name, cancel to use the default group \r
+ name. </em><strong><br>\r
+ </strong></li>\r
+ <li><strong>Remove Group<br>\r
+ </strong><em>This will undefine the selected group. </em><strong> <br>\r
+ </strong></li>\r
+ <li><strong>Group Colour<br>\r
+ </strong><em>Sets the <a href="../colourSchemes/index.html">colour</a> \r
+ of the group.</em><strong> <br>\r
+ </strong></li>\r
+ <li><strong>Boxes<br>\r
+ </strong><em>If selected the background of a residue within the selected \r
+ group will be coloured according to the assigned colour scheme.</em><strong> \r
+ <br>\r
+ </strong></li>\r
+ <li><strong> Text<br>\r
+ </strong><em>If selected the selected group will display text. </em><strong><br>\r
+ </strong></li>\r
+ <li><strong>Colour Text<br>\r
+ </strong><em>If selected the selected group will display text in a colour \r
+ slightly darker than the background colour of that residue.</em><strong><br>\r
+ </strong></li>\r
+ <li><strong>Border Colour <br>\r
+ </strong><em>Selecting this will display a "Colour Chooser" \r
+ window. Select a colour than press OK to set the border colour of a group.</em><strong><br>\r
+ </strong></li>\r
+ </ul>\r
+ </li>\r
+ <li><strong>Sequence <br>\r
+ </strong><em>This menu is only visible if you right-click on a sequence name. \r
+ </em> \r
+ <ul>\r
+ <li><strong>Edit Name<br>\r
+ </strong><em>You may edit the name of each sequence. A window will be \r
+ displayed asking for a new sequence name to be entered. Press OK to accept \r
+ your edit.</em><strong><br>\r
+ </strong></li>\r
+ <li><strong>View PDB Structure<br>\r
+ </strong><em>In the current version you will first need to select "View \r
+ -> Sequence Features" before associating a PDB file with a sequence. \r
+ <br>\r
+ If the sequence has a PDB file associated with it Jalview will display \r
+ a 3D interactive viewer of the file. </em><strong><br>\r
+ <br>\r
+ </strong></li>\r
+ </ul>\r
+ </li>\r
</ul>\r
</body>\r
</html>\r