+++ /dev/null
-<html>
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ 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
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- * 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