<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/Description<br>\r
+ </strong><em>You may edit the name and description of each sequence. A \r
+ window will be displayed asking for a new sequence name and sequence description \r
+ to be entered. Press OK to accept your edit. To save sequence descriptions, \r
+ you must save in Fasta, PIR or Jalview File format.</em><strong><br>\r
+ </strong></li>\r
+ <li><strong>View PDB Structure<br>\r
+ </strong><em>\r
+ If the sequence has a PDB file associated with it Jalview will display \r
+ a 3D interactive viewer of the file.<br>\r
+This entry is only present if the sequence has an\r
+ <a href="../features/viewingpdbs.html">associated PDB structure</a>.\r
+ If you can't see this entry for your sequence, and the sequence name\r
+ is a uniprot identifier, then try enabling the "View \r
+ -> Sequence Features" and opening the popup menu again.</em>\r
+ </li>\r
+ </ul>\r
+ </li>\r
+ <li><strong><em>Link</em></strong><br>\r
+ <em>This menu item lists all links which have been set up in the <a href="../features/preferences.html">Preferences</a> \r
+ Connections tab. It is only displayed when you right click (Apple click) on \r
+ a sequence id. </em><strong><br>\r
+ <br>\r
+ </strong></li>\r
</ul>\r
</body>\r
</html>\r
git://source.jalview.org / jalview.git / blobdiff