-<html>\r
-<head><title>PDB Viewer</title></head>\r
-<body>\r
-<p><strong>Viewing PDB Structures</strong></p>\r
-<p>Jalview has a simple 3D structure viewer which can load PDB files and associate \r
- the structure with a sequence in an alignment. </p>\r
-<p>There are 2 ways to load and associate a PDB file into Jalview application.</p>\r
-<ul>\r
- <li>Select "<a href="seqfeatures.html">Sequence Features</a>" from \r
- the "View" menu. This will attempt to match your sequences with \r
- the Uniprot database first by name, then by sequence. The same process will \r
- make note of any PDB files associated with each sequence. </li>\r
- <li>Select "<a href="seqfetch.html">Fetch Sequence</a>" from an alignment \r
- window or from the main desktop "File" menu. In the popup window \r
- which appears, select PDB as the database and enter your known PDB id. If \r
- you know which chain you wish to retrieve, append the chain id after a colon \r
- eg 1GAQ:B</li>\r
-</ul>\r
-<p>Note the applet can only load PDB files by copying and pasting the text into \r
- the popup window which appears when "Show PDB Structure" is selected \r
- after right clicking on a sequence name.</p>\r
-<p>To see a particular structure, right click on a sequence name and from the \r
- popup menu select "Sequence -> View PDB Entry". </p>\r
-<p>The PDB Structure viewer will perform a pairwise alignment of your sequence \r
- and each PDB chain sequence. To view the results of the mapping, select "File \r
- -> View Mapping" from the structure viewer window. </p>\r
-<p>Moving the mouse over the structure will highlight the residue in the alignment \r
- window, and vice versa.</p>\r
-<p>"Colour by Charge/Cysteine" will colour all Aspartate and Glutamate \r
- residues red, Lysine and Arginine will be blue and Cysteine residues will be \r
- coloured yellow.</p>\r
-<p><em>Tips for Viewing Structures</em></p>\r
-<ul>\r
- <li>Colour By Sequence follows the exact colours of the alignment window, including \r
- sequence features. Thus you can easily view Uniprot sequence features, eg \r
- helix or metal binding sites on both the alignment and structure viewer.</li>\r
- <li>Deselect Colours->Show All Chains in order to view only the mapped chain. \r
- </li>\r
- <li>Use Wireframe, without depthcue, and without Z Buffering in order to accelerate \r
- the rendering of the structure. </li>\r
- <li>You can save an image of your structure as a PNG or EPS file.</li>\r
- <li>Use the cursor keys Up and Down arrow to zoom in and zoom out</li>\r
-</ul>\r
-</body>\r
-</html>\r
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
+ *
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<head>
+<title>PDB Viewer</title>
+</head>
+<body>
+ <p>
+ <strong>The Jalview internal PDB Viewer</strong><br> Since
+ Jalview 2.3, the <a href="jmol.html">Jmol PDB Viewer</a> is the main
+ method for <a href="viewingpdbs.html">viewing PDB structures</a>.
+ The documentation below concerns the original Jalview PDB viewer,
+ which is only used in situations where Jmol is unavailable or cannot
+ operate.
+ </p>
+ <p>
+ <strong>The PDB Viewer Window</strong>
+ <p>
+ This interactive structure viewing window is opened by selecting
+ entries from the <strong>"Structure→"</strong>
+ submenu of the <a href="../menus/popupMenu.html">sequence id
+ pop-up menu</a>. The internal PDB viewer is not able to show
+ superpositions, so no other options are provided. Structures can
+ only be viewed for sequences which have an <a
+ href="viewingpdbs.html"
+ >associated PDB structure</a>, and the PDB Viewer will only be
+ associated with the particular alignment view from which it was
+ opened.
+ </p>
+ <p>
+ <strong>Controls</strong>
+ </p>
+ <p>The structure is rendered as an alpha-carbon trace. Moving the
+ mouse over the structure brings up tooltips with a residue name and
+ PDB sequence position. If a mapping exists to a residue in the
+ associated sequence, then this will be highlighted in the associated
+ view in its alignment window, and vice versa for viewing the
+ coordinates associated with a particular residue in the sequence in
+ a particular view on the alignment.</p>
+ <p>Selecting a residue highlights its associated sequence residue
+ and alpha carbon location.</p>
+ <p>
+ <table>
+ <tr>
+ <td><strong>Action</strong></td>
+ <td><strong>Windows</strong></td>
+ <td><strong>Unix</strong></td>
+ <td><strong>Mac/OSX</strong></td>
+ </tr>
+ <tr>
+ <td>Select/<br> Deselect<br> Residue
+ </td>
+ <td>Left Click</td>
+ <td>Left Click</td>
+ <td>Click</td>
+ </tr>
+ <tr>
+ <td>Rotate View</td>
+ <td>Left Click and Drag</td>
+ <td>Left Click and Drag</td>
+ <td>Click and Drag</td>
+ </tr>
+ <tr>
+ <td>Roll View</td>
+ <td>Right Click and drag</td>
+ <td>Right Click and Drag</td>
+ <td>TODO</td>
+ </tr>
+ <tr>
+ <td>Move Origin</td>
+ <td>Middle-Button and Drag</td>
+ <td>Middle-Button and Drag</td>
+ <td>TODO</td>
+ </tr>
+ <tr>
+ <td>Zoom In</td>
+ <td>Up Arrow</td>
+ <td>Up Arrow</td>
+ <td>Up Arrow</td>
+ </tr>
+ <tr>
+ <td>Zoom Out</td>
+ <td>Down Arrow</td>
+ <td>Down Arrow</td>
+ <td>Down Arrow</td>
+ </tr>
+ </table>
+ </p>
+ <p>There are three menus:
+ <ul>
+ <li><Strong>File<br>
+ </strong>
+ <ul>
+ <li><strong>Save As<br>
+ </strong><em>Saves the current view as an EPS or PNG file.</em></li>
+ <li><strong>View Mapping<br>
+ </strong><em> Opens a text window showing the alignment between the
+ residues corresponding to alpha-carbon atoms in the PDB
+ structure and the residues in the associated sequence.</em></li>
+ </ul></li>
+ <li><strong>Colours<br>
+ </strong>
+ <ul>
+ <li><strong>By Sequence<br>
+ </strong><em> Colours each residue in the structure with the colour
+ of its corresponding residue in the associated sequence as
+ rendered in the associated alignment view, including any
+ Uniprot sequence features or region colourings.<br>
+ Residues which only exist in the PDB structure are coloured
+ white if they are insertions (relative to the associated
+ sequence in the alignment) and grey if they are N or C
+ terminal flanks outside the region mapped to the alignment
+ window's sequence.
+ </em></li>
+ <li><strong>By Chain<br>
+ </strong><em> Assigns a random colour to each PDB chain.</em>
+ <li><strong>Charge & Cysteine<br>
+ </strong><em> Highlights cysteines in yellow, anionic (Aspartic Acid
+ or Glutamic Acid) residues in red, and cationic (Lysine or
+ Arginine) residues in blue.</em></li>
+ <li><strong><em>Standard and User Defined
+ Jalview colourschemes.<br>
+ </em></strong> The remaining entries apply the colourschemes available from
+ the standard and user defined <a
+ href="../colourSchemes/index.html"
+ >amino acid colours</a>.</em></li>
+ </ul></li>
+ <li><strong>View<br>
+ </strong><em> These options can be turned off to improve performance
+ when viewing large structures, some at the expense of visual
+ clarity.</em>
+ <ul>
+ <li><strong>Wireframe<br>
+ </strong><em> Draws thin lines rather than thick lines for the
+ alpha-carbon trace.</em></li>
+ <li><strong>Depthcue<br>
+ </strong><em>Shades the structure so parts of the structure near the
+ front of the view are brighter than those further away.</em></li>
+ <li><strong>Z Buffering<br>
+ </strong><em> Applies depth sorting to correctly render occluded
+ regions of the backbone trace.</em></li>
+ <li><strong>Show All Chains<br>
+ </strong><em> When turned on, shows all chains in the PDB file, not
+ just the one associated with a sequence in the alignment
+ window.</em></li>
+ <!-- NOT YET IMPLEMENTED <li><strong>Associate View</strong><br>
+ Change which view on the associated sequence's alignment is to be
+ associated with the PDB viewer.-->
+ </ul></li>
+ </ul>
+ </p>
+ <p>
+ <strong>Notes for PDB Viewing in the Jalview Applet</strong>
+ <p>The applet can only load PDB files by copying and pasting the
+ text into the popup window which appears when "Show PDB
+ Structure" is selected after right clicking on a sequence name.</p>
+</body>
+</html>
git://source.jalview.org / jalview.git / blobdiff