--- /dev/null
+<html>\r
+<!--\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)\r
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
+ * \r
+ * This file is part of Jalview.\r
+ * \r
+ * Jalview is free software: you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License \r
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\r
+ * \r
+ * Jalview is distributed in the hope that it will be useful, but \r
+ * WITHOUT ANY WARRANTY; without even the implied warranty \r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+ * PURPOSE. See the GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
+-->\r
+<head>\r
+<title>The VARNA RNA Viewer</title>\r
+</head>\r
+<body>\r
+<p><strong>The VARNA RNA Viewer</strong></p>\r
+<p>Since Jalview\r
+2.7.1, <a href="http://varna.lri.fr/index.html">VARNA</a> has been\r
+integrated into Jalview for interactively viewing structures opened by\r
+selecting the <strong>"Structure→View\r
+Structure:"</strong> option in\r
+the <a href="../menus/popupMenu.html">sequence id pop-up menu</a> (if\r
+you can't see this, then no RNA structure is associated with your\r
+sequence or alignment. In the pop-up menu all structures that\r
+are associated with this sequence and all sequences that are\r
+associated with the alignment are available.\r
+\r
+<p><strong>Different structures</strong></p>\r
+<ul>\r
+ <li>\r
+ <b>Alignment structures</b>:\r
+ Structures associated with the alignment are marked by having "consensus" attached to their name. VARNA contains two different entries for consensus structures.\r
+ <ul>\r
+ <li>Consensus structure: the individual sequence folded into the consensus structure</li>\r
+ <li>Trimed consensus structure: the individual sequence\r
+ folded into the the gap-free consensus structure. That means all\r
+ columns that contained gaps in the individual sequence were\r
+ removed. If this breaks a base-pair the pairing is removed also.\r
+ This can be considered as an approximation for the individual structure.\r
+ </ul>\r
+ </li>\r
+ <li>\r
+ <b>Individual structures</b>:\r
+ this is a structure associated with the individual sequence and therefore not related to the alignment \r
+ </li>\r
+\r
+<p><strong>Controls</strong><br>\r
+<ul>\r
+<li>Rotate view - Left Click and drag</li>\r
+<li>Zoom in - Press '+'</li>\r
+<li>Zoom out - Press '-'</li>\r
+<li>Choose a different structure - Left click on structure in the left hand panel</li>\r
+<li>Highlighting bases - Move mouse over columns in the Jalview alignment panel</li>\r
+</ul>\r
+\r
+<p><strong>Functionality provided by Jmol</strong></p>\r
+<p>VARNA's own functions are accessed by right-clicking in the\r
+structure display area. That will open the VARNA pop-up menu,\r
+which provides access to a number of features like different draw algorithm, color highlighting or annotations. \r
+</p>\r
+<p><strong>More Information</strong></p>\r
+<p>VARNA is a very powerful RNA viewer on it's own. Only the\r
+essentials have been described here - the interested reader is\r
+referred to <a href="http://varna.lri.fr/usermanual.html">VARNA's own\r
+comprehensive online documentation</a>.</p>\r
+</body>\r
+</html>\r
git://source.jalview.org / jalview.git / blobdiff