<mapID target="viewingpdbs" url="html/features/viewingpdbs.html"/>
<mapID target="pdbmcviewer" url="html/features/pdbviewer.html"/>
<mapID target="pdbjmol" url="html/features/jmol.html"/>
+ <mapID target="varna" url="html/features/varna.html"/>
<mapID target="preferences" url="html/features/preferences.html"/>
<mapID target="commandline" url="html/features/commandline.html"/>
<mapID target="clarguments" url="html/features/clarguments.html"/>
<mapID target="calcs.alquality" url="html/calculations/quality.html"/>
<mapID target="calcs.alconserv" url="html/calculations/conservation.html"/>
+ <mapID target="calcs.alstrconsensus" url="html/calculations/structureconsensus.html"/>
<mapID target="calcs.consensus" url="html/calculations/consensus.html"/>
<mapID target="nucleicAcids" url="html/na/index.html"/>
<br> <a href="html/calculations/redundancy.html" target=bodyframe>Remove Redundancy</a>
<br> <a href="html/features/annotation.html" target=bodyframe>Alignment Annotations</a>
<br> <a href="html/calculations/conservation.html" target=bodyframe>Conservation</a>
-<br> <a href="html/calculations/structureconservation.html" target=bodyframe>RNA Structure Conservation</a>
<br> <a href="html/calculations/quality.html" target=bodyframe>Quality</a>
<br> <a href="html/calculations/consensus.html" target=bodyframe>Consensus</a>
+<br> <a href="html/calculations/structureconsensus.html" target=bodyframe>RNA Structure Consensus</a>
<br> <a href="html/features/annotationsFormat.html" target=bodyframe>Annotations File Format</a>
<br> <a href="html/features/viewingpdbs.html" target=bodyframe>Viewing PDB Files</a>
<br> <a href="html/features/jmol.html" target=bodyframe>Jmol Viewer</a>
<br> <a href="html/features/pdbviewer.html" target=bodyframe>Simple PDB Viewer</a>
+<br> <a href="html/features/varna.html" target=bodyframe>Viewing RNA structures</a>
<br> <a href="html/vamsas/index.html" target=bodyframe>VAMSAS Data Exchange</a>
<br> <a href="html/menus/index.html" target=bodyframe>Window Menus</a>
<br> <a href="html/menus/desktopMenu.html" target=bodyframe>Desktop Window</a>
<tocitem text="Multiple Views" target="multipleviews"/>
<tocitem text="Viewing Trees" target="treeviewer" expand="false"/>
<tocitem text="Fetching Sequences" target="seqfetch"/>
- <tocitem text="Nucleic Acid Support" target="nucleicAcids" expand="false"></tocitem>
+ <tocitem text="Nucleic Acid Support" target="nucleicAcids" expand="false">
+ <tocitem text="Viewing RNA structure" target="varna" />
+ <tocitem text="RNA Structure Consensus" target="calcs.alstrconsensus"/>
+ <tocitem text="RNA Helices coloring" target="colours.rnahelices"/>
+ </tocitem>
<tocitem text="Sequence Features" target="seqfeatures" expand="false">
<tocitem text="Sequence Feature Settings" target="seqfeatures.settings"/>
<tocitem text="Sequence Features File" target="features.fileformat"/>
<tocitem text="Remove Redundancy" target="redundancy"/>
</tocitem>
<tocitem text="Alignment Annotations" target ="alannotation" expand="false">
- <tocitem text="Conservation" target="calcs.alconserv"/>
- <tocitem text="RNA Structure Conservation" target="calcs.alstrconserv"/>
+ <tocitem text="Conservation" target="calcs.alconserv"/>
<tocitem text="Quality" target="calcs.alquality"/>
<tocitem text="Consensus" target="calcs.consensus"/>
+ <tocitem text="RNA Structure Consensus" target="calcs.alstrconsensus"/>
<tocitem text="Annotations File Format" target="annotations.fileformat"/>
</tocitem>
<tocitem text="Viewing PDB Files" target="viewingpdbs" expand="false">
<tocitem text="Jmol Viewer" target="pdbjmol"/>
<tocitem text="Simple PDB Viewer" target="pdbmcviewer"/>
</tocitem>
+ <tocitem text="Viewing RNA structures" target="varna" expand="false"> </tocitem>
<tocitem text="VAMSAS Data Exchange" target="vamsas">
<!-- what can Jalview share with other apps -->
<!-- what other apps exist -->
<p>Select the <strong>"Copy Consensus Sequence"</strong> entry from
the consensus annotation label to copy the alignment's consensus sequence to the
clipboard.
+
+<p><strong>Sequence logo</strong></p>
+By clicking on the label you can also activate the sequence logo. It
+indicates the relative amount of residues per column which can be
+estimated by it's size in the logo. The tooltip of a column gives the
+exact numbers for all occuring residues.
</p>
</body>
</html>
--- /dev/null
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+-->
+<head><title>Alignment RNA Structure Consensus Annotation</title></head>
+<body><p><strong>Alignment RNA Structure Consensus Annotation</strong></p>
+
+<p>The RNA structure consensus displayed below the alignment is the
+percentage of valid base pairs per column. It is calculated in
+relation to a secondary structure and just paired columns are
+calculated. The canonical Watson-Crick base pairings (A-T/U, G-C) and
+the wobble base pair (G-T/U) are regarded as valid pairings.<br>
+The amount of valid base pairs is indicated by the profile in the
+Alignment Annotation row.<br>
+By default this calculation includes gaps in columns. You can choose
+to ignore gaps in the calculation by right clicking on the label
+"StrConsensus" to the left of the structure consensus bar
+chart.<br>
+
+<p><strong>Structure logo</strong></p>
+By clicking on the label you can also activate the structure logo. It is very
+similar to a sequence logo but counts the numbers of base pairs. There
+are two residues per column, the actual column and the interacting
+base. The opening bracket is always the one on the left side.<br>
+Like sequence logos the relative amount of a specific base pair can be
+estimated by it's size in the logo. The tooltip of a column gives the
+exact numbers for all occuring valid base pairs.
+</p>
+</body>
+</html>
+++ /dev/null
-<html>
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
--->
-<head><title>Alignment RNA Structure Conservation Annotation</title></head>
-<body><p><strong>Alignment RNA Structure Conservation Annotation</strong></p>
-<p>This is an automatically calculated quantitative alignment
-annotation which measures the number of conserved base pairs in
-relation to a secondary structure. The canonical Watson-Crick base
-pairings (A-T/U, G-C) and the wobble base pair (G-T/U) are regarded as
-valid pairings.<br>
-The amount of valid base pairs is indicated by the profile in the Alignment Annotation row.
-</body>
-</html>
<p><strong>The Jmol PDB Viewer</strong></p>\r
<p>Since Jalview 2.3, <a href="http://jmol.sourceforge.net/">Jmol</a>\r
has been integrated into Jalview for interactively viewing structures\r
-opened by selecting the <strong>"Sequence→View PDB\r
+opened by selecting the <strong>"Structure→View PDB\r
entry:"</strong> option in the <a href="../menus/popupMenu.html">sequence\r
id pop-up menu</a> (if you can't see this, then you need to <a\r
href="viewingpdbs.html">associate a PDB structure</a> with the\r
--- /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 / commitdiff