<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
+<p><strong>The PDB Viewer Window</strong>\r
+<p>This interactive structure viewing window is opened by selecting the\r
+<strong>"Sequence→View PDB\r
+entry:"</strong> entry in the <a\r
+href="../menus/popupMenu.html">sequence id pop-up menu</a>. This can only be\r
+done for sequences which have an <a href="viewingpdbs.html">associated\r
+PDB structure</a>.</p>\r
+<p><strong>Controls</strong></p>\r
+<p>The structure is rendered as an alpha-carbon trace. \r
+Moving the mouse over the structure brings up tooltips with a\r
+residue name and PDB sequence position. If a mapping exists to a\r
+residue in the associated sequence, then this will be highlighted in\r
+the alignment window, and vice versa for viewing the coordinates\r
+associated with a particular residue in the sequence.</p>\r
+<p>Selecting a residue highlights its associated sequence residue and\r
+alpha carbon location.</p>\r
+<p><table>\r
+<tr><td><strong>Action</strong></td><td><strong>Windows</strong></td><td><strong>Unix</strong></td><td><strong>Mac/OSX</strong></td></tr>\r
+<tr><td>Select/<br>Deselect<br>Residue</td><td>Left Click</td><td>Left\r
+Click</td><td>Click</td></tr>\r
+<tr><td>Rotate View</td><td>Left Click and Drag</td><td>Left Click and\r
+Drag</td><td>Click and Drag</td></tr>\r
+<tr><td>Roll View</td><td>Right Click and drag</td><td>Right Click and\r
+Drag</td><td>TODO</td></tr>\r
+<tr><td>Move Origin</td><td>Middle-Button and\r
+Drag</td><td>Middle-Button and Drag</td><td>TODO</td></tr>\r
+<tr><td>Zoom In</td><td>Up Arrow</td><td>Up Arrow</td><td>Up\r
+Arrow</td></tr>\r
+<tr><td>Zoom Out</td><td>Down Arrow</td><td>Down Arrow</td><td>Down Arrow</td></tr>\r
+</table>\r
+</p>\r
+<p>There are three menus:\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
+<li><Strong>File<br></strong><ul>\r
+<li><strong>Save As<br></strong><em>Saves the current view as an EPS or PNG file.</em>\r
+</li>\r
+<li><strong>View Mapping<br></strong><em>\r
+Opens a text window showing the alignment between the residues\r
+corresponding to alpha-carbon atoms in the PDB structure and the\r
+residues in the associated sequence.</em>\r
+</li>\r
</ul>\r
-<p>Note the applet can only load PDB files by copying and pasting the text into \r
+</li>\r
+<li><strong>Colours<br></strong><ul>\r
+<li><strong>By Sequence<br></strong><em>\r
+Colours each residue in the structure with the colour of its\r
+corresponding residue in the associated sequence as rendered in the\r
+alignment window, including any Uniprot sequence features or region\r
+colourings.<br>Residues which only exist in the PDB structure are\r
+coloured white if they are insertions (relative to the associated\r
+sequence in the alignment) and grey if they are N or C terminal\r
+flanks outside the region mapped to the alignment window's sequence.</em></li>\r
+<li><strong>By Chain<br></strong><em>\r
+Assigns a random colour to each PDB chain.</em>\r
+<li><strong>Charge & Cysteine<br></strong><em>\r
+Highlights cysteines in yellow, anionic (Aspartic Acid or Glutamic Acid) residues in red, and\r
+cationic (Lysine or Arginine) residues in blue.</em>\r
+</li>\r
+<li><strong><em>Standard and User Defined Jalview colourschemes.<br></em></strong>\r
+The remaining entries apply the colourschemes available from the\r
+standard and user defined <a href="../colourSchemes/index.html">amino acid colours</a>.</em>\r
+</li>\r
+</ul>\r
+</li>\r
+<li><strong>View<br></strong><em>\r
+These options can be turned off to improve performance when viewing\r
+large structures, some at the expense of visual clarity.</em><ul>\r
+<li><strong>Wireframe<br></strong><em>\r
+Draws thin lines rather than thick lines for the\r
+alpha-carbon trace.</em>\r
+</li><li><strong>Depthcue<br></strong><em>Shades the structure so parts of the structure near\r
+the front of the view are brighter than those further away.</em>\r
+</li><li><strong>Z Buffering<br></strong><em>\r
+Applies depth sorting to correctly render occluded regions of the\r
+backbone trace.</em>\r
+</li>\r
+<li><strong>Show All Chains<br></strong><em>\r
+When turned on, shows all chains in the PDB file, not just the one\r
+associated with a sequence in the alignment window.</em>\r
+</li>\r
+</ul>\r
+</li>\r
+</ul>\r
+</p>\r
+<p><strong>Notes for PDB Viewing in the Jalview Applet</strong>\r
+<p>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
git://source.jalview.org / jalview.git / commitdiff