<mapID target="seqfeatcreat" url="html/features/creatinFeatures.html"/>
<mapID target="seqfeatures.settings" url="html/features/featuresettings.html"/>
<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="preferences" url="html/features/preferences.html"/>
<mapID target="commandline" url="html/features/commandline.html"/>
<mapID target="clarguments" url="html/features/clarguments.html"/>
<tocitem text="Jalview Documentation" target="home" expand="true" >
<tocitem text="What's new" target="new" expand="true">
<tocitem text="Release History" target="release"/>
+ <tocitem text="PDB Viewing with Jmol" target="pdbjmol"/>
<tocitem text="Mapping between Sequences" target="seqmappings"/>
<tocitem text="Coding Region Sequence Features" target="cdnafeatures"/>
</tocitem>
<tocitem text="Input / Output" target="io"/>
<tocitem text="Making figures" target="export"/>
<tocitem text="Hidden Regions" target="hiddenRegions"/>
- <tocitem text="Viewing PDB Files" target="viewingpdbs"/>
<tocitem text="Multiple Views" target="multipleviews"/>
<tocitem text="Sequence Features" target="seqfeatures" expand="false">
<tocitem text="Sequence Feature Settings" target="seqfeatures.settings"/>
<tocitem text="Consensus" target="calcs.consensus"/>
<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="Window Menus" target="menus" expand="false">
<tocitem text="Desktop Window" target="desktopMenu"/>
<tocitem text="Alignment Window" target="alMenu">
--- /dev/null
+<html>\r
+<head>\r
+<title>The Jmol PDB Viewer</title>\r
+</head>\r
+<body>\r
+<p><strong>The Jmol PDB Viewer</strong>\r
+<p>The interactive structure viewing window is opened by selecting\r
+the <strong>"Sequence→View PDB entry:"</strong> entry in\r
+the <a href="../menus/popupMenu.html">sequence id pop-up menu</a>. This\r
+can only be done for sequences which have an <a href="viewingpdbs.html">associated\r
+PDB structure</a>.\r
+<p>Since Jalview 2.3, <a href="http://jmol.sourceforge.net/">Jmol</a>\r
+has been integrated into Jalview. It is automatically used by the\r
+application, and should also run in the applet in all latest web\r
+browsers. If jmol is not available, then the original <a\r
+href="pdbviewer.html">internal pdb viewer</a> will be used as a fallback.\r
+</p>\r
+<p><strong>Controls</strong></p>\r
+<p>The structure is by default rendered as a ribbon diagram. Moving the\r
+mouse over the structure brings up tooltips giving the residue name,\r
+PDB residue number and chain code, atom name and number\r
+([RES]Num:Chain.AtomName#AtomNumber). If a mapping exists to a residue\r
+in any associated sequences, then this will be highlighted in each\r
+one's alignment window. The converse also occurs - moving the mouse\r
+over an associated residue in an alignment window highlights the associated\r
+atoms in the displayed structures.</p>\r
+<p>Selecting a residue highlights its associated sequence residue\r
+and alpha carbon location. Double clicking an atom allows distances to\r
+be measured from it to any other atom in the structure.</p>\r
+<p>\r
+<table>\r
+ <tr>\r
+ <td><strong>Action</strong></td>\r
+ <td><strong>Windows</strong></td>\r
+ <td><strong>Unix</strong></td>\r
+ <td><strong>Mac/OSX</strong></td>\r
+ </tr>\r
+ <tr>\r
+ <td>Rotate View</td>\r
+ <td>Left Click and Drag</td>\r
+ <td>Left Click and Drag</td>\r
+ <td>Click and Drag</td>\r
+ </tr>\r
+ <tr>\r
+ <td>Zoom</td>\r
+ <td>Shift + Left Click<br>drag mouse up or down</td>\r
+ <td>Shift + Left Click<br>or middle button<br>drag\r
+ mouse up or down</td>\r
+ <td>Left-Alt + Click and drag mouse up or down</td>\r
+ </tr>\r
+ <tr>\r
+ <td>Select/<br>\r
+ Deselect<br>\r
+ Residue</td>\r
+ <td>Left Click</td>\r
+ <td>Left Click</td>\r
+ <td>Click</td>\r
+ </tr>\r
+ <tr>\r
+ <td>Roll View</td>\r
+ <td>Shift + Left Click<br>drag mouse to left or\r
+ right</td>\r
+ <td>Shift + Left Click<br>or middle button<br>drag mouse to left or right</td>\r
+ <td>Left-Alt + Click and drag mouse to left or right</td>\r
+ </tr>\r
+ <tr>\r
+ <td>Move Origin</td>\r
+ <td>Shift+Control+Left Click<br>or Middle Button<br>\r
+ + Drag</td>\r
+ <td>Middle-Button<br>and<br>drag</td>\r
+ <td>Shift+Control+Left Click<br>or Middle Button<br>\r
+ and drag</td>\r
+ </tr>\r
+ <tr>\r
+ <td>Jmol Menu</td>\r
+ <td>Right-Click</td>\r
+ <td>Right-Click</td>\r
+ <td>Apple-Click</td>\r
+ </tr>\r
+</table>\r
+</p>\r
+<p>The window has four menus:\r
+<ul>\r
+ <li><Strong>File<br>\r
+ </strong>\r
+ <ul>\r
+ <li><strong>Save As<br>\r
+ </strong><em>Save the displayed PDB File, or the current view as an EPS or PNG file.</em></li>\r
+ <li><strong>View Mapping<br>\r
+ </strong><em> Opens a text window showing the alignment between the\r
+ residues corresponding to alpha-carbon atoms in the PDB structure and\r
+ the residues in the associated sequence.</em></li>\r
+ </ul>\r
+ </li>\r
+ <li><strong>View</strong>\r
+ <ul>\r
+ <li><strong>Show Chains<br></strong><em>Select which of the PDB\r
+ file's chains are to be displayed.</em>\r
+ </li>\r
+ </ul>\r
+ <li><strong>Colours<br>\r
+ </strong>\r
+ <ul>\r
+ <li><strong>By Sequence<br>\r
+ </strong><em> Colours each residue in the structure with the colour of its\r
+ corresponding residue in the associated sequence as rendered in the\r
+ associated alignment view, including any Uniprot sequence features or\r
+ region colourings.<br>\r
+ Residues which only exist in the PDB structure are coloured white if\r
+ they are insertions (relative to the associated sequence in the\r
+ alignment) and grey if they are N or C terminal flanks outside the\r
+ region mapped to the alignment window's sequence.</em></li>\r
+ <li><strong>By Chain<br>\r
+ </strong><em> Assigns a random colour to each PDB chain.</em>\r
+ <li><strong>Charge & Cysteine<br>\r
+ </strong><em> Highlights cysteines in yellow, anionic (Aspartic Acid or\r
+ Glutamic Acid) residues in red, and cationic (Lysine or Arginine)\r
+ residues in blue.</em></li>\r
+ <li><strong>Standard and User Defined Jalview\r
+ colourschemes.<br>\r
+ </strong><em>The remaining entries apply the colourschemes available from the\r
+ standard and user defined <a href="../colourSchemes/index.html">amino\r
+ acid colours</a>.</em></li>\r
+ </ul>\r
+ </li>\r
+ <li><strong>Help<br></strong><ul><li><strong>Jmol Help<br></strong><em>Access the Jmol Help\r
+ documentation in a new browser window.</em>\r
+ </li>\r
+ </ul>\r
+</li></ul>\r
+</p>\r
+<p><strong>Functionality provided by Jmol</strong>\r
+</p><p>The Jmol menu provides access to a number of features for\r
+controlling the colour and display of molecules, adding measurements and\r
+labels, plotting surfaces, and display animation. The 'Set Picking'\r
+menu controls the behaviour of single and double mouse clicking on the\r
+structure.</p>\r
+<p>The state of each Jmol display is stored within <a\r
+href="jalarchive.html">jalview archives</a> using Jmol's own state\r
+storage format. This means that any Jmol visualization effects that\r
+you add beyond those provided by Jalview will be able to be stored and\r
+recovered along with the displayed alignments in Jalview.\r
+</p><p><strong>More Information</strong>\r
+</p><p>Jmol is a sophisticated program in its own right, with its own\r
+command console and scripting language. Only the essentials have been\r
+described here - the interested reader is referred to \r
+<a href="http://jmol.sourceforge.net/docs/">Jmol's own comprehensive\r
+online documenation</a>.</p></p>\r
+</body>\r
+</html>\r
<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
the <strong>"Sequence→View PDB entry:"</strong> entry in
-<html>\r
-<head><title>PDB Viewing</title></head>\r
-<body>\r
-<p><strong>Viewing PDB Structures</strong></p>\r
-<p>Jalview has a simple <a href="pdbviewer.html">3D structure viewer</a> which \r
- can visualize polypeptide backbone structures associated with a sequence in \r
- a particular alignment view. It is accessed via the <strong>"Strucutre→View \r
- PDB entry:"</strong> entry from the sequence's <a\r
- href="../menus/popupMenu.html">pop-up menu</a>.</p>\r
-<p>Since Jalview 2.3, Jmol has been integrated into the application and will also \r
- run in the applet in all latest web browsers. For more help using Jmol, see \r
- <a href="http://jmol.sourceforge.net/docs/JmolUserGuide/">http://jmol.sourceforge.net/docs/JmolUserGuide/</a> \r
-</p>\r
-<p>To associate PDB files with a sequence, right click on a sequence ID and select \r
- "Structure<strong>→</strong> Associate Structure with Sequence", \r
- and one of the submenus:</p>\r
-<ul>\r
- <li>From File - You can load a PDB file from the local machine or network and \r
- associate it with the selected sequence. PDB files associated in this way \r
- will also be saved in the <a href="jalarchive.html">Jalview Archive file</a>. <br>\r
- </li>\r
- <li>Enter PDB Id - Jalview will use WSDBFetch, provided by the EBI, to fetch \r
- the PDB file with the entered Id.<br>\r
- </li>\r
- <li>Discover PDB Ids - Jalview uses WSDBFetch, provided by the EBI, to discover \r
- PDB ids for all the sequences in the alignment which have valid Uniprot names \r
- / accession ids. </li>\r
-</ul>\r
-<p><strong>Note:</strong> You can retrieve sequences from the PDB using the <a\r
- href="seqfetch.html">Sequence Fetcher</a>. Any sequences retrieved with this \r
- service are automatically associated with their source database entry. For PDB \r
- sequences, simply select PDB as the database and enter your known PDB id (appended \r
- with ':' and a chain code, if desired).</p>\r
- <p>Sequences which have PDB File associations are annotated with sequence features \r
- from the group 'PDBFile' giving the corresponding PDB Residue Number for each \r
- mapped residue in the seuqence. The display of these features is controlled through\r
- the <strong>"View→Sequence Features"</strong> menu item and the \r
- <a href="featuresettings.html">Feature Settings dialog box</a>.</p> \r
-<p>See the <a\r
-href="pdbviewer.html">PDB Viewer</a> help page for more information. </p> </p>\r
-</body>\r
-</html>\r
+<html>
+<head><title>PDB Viewing</title></head>
+<body>
+<p><strong>Viewing PDB Structures</strong></p>
+<p>Jalview can view protein structures associated with a sequence via the <strong>"Structure→View
+ PDB entry:"</strong> entries from a sequence's <a
+ href="../menus/popupMenu.html">pop-up menu</a>. This will open an
+ interactive display of the structure in a new window, or prompt you
+ to associate the sequence with an existing view of the selected
+ structure. See the <a href="jmol.html">Jmol PDB viewer</a> help page
+ for more information about the display.
+</p>
+<p>To associate PDB files with a sequence, right click on a sequence ID and select
+ "Structure<strong>→</strong> Associate Structure with Sequence",
+ and one of the submenus:</p>
+<ul>
+ <li>From File - You can load a PDB file from the local machine or network and
+ associate it with the selected sequence. PDB files associated in this way
+ will also be saved in the <a href="jalarchive.html">Jalview Archive file</a>. <br>
+ </li>
+ <li>Enter PDB Id - Jalview will use WSDBFetch, provided by the EBI, to fetch
+ the PDB file with the entered Id.<br>
+ </li>
+ <li>Discover PDB Ids - Jalview uses WSDBFetch, provided by the EBI, to discover
+ PDB ids for all the sequences in the alignment which have valid Uniprot names
+ / accession ids. </li>
+</ul>
+<p><strong>Importing PDB Entries or files in PDB format</strong><br>
+You can retrieve sequences from the PDB using the <a
+ href="seqfetch.html">Sequence Fetcher</a>. Any sequences retrieved with this
+ service are automatically associated with their source database entry. For PDB
+ sequences, simply select PDB as the database and enter your known PDB id (appended
+ with ':' and a chain code, if desired).
+<br>Jalview will also read PDB files directly. Simply load in the file
+as you would an alignment file. The sequences of any peptide chains
+will be extracted from the file and viewed in the alignment window.
+<br><em>Note for jalview applet users: due to the applet security
+constraints, PDB Files can currently only be imported by cut and paste
+of the PDB file text into the text box opened by the 'From File' entry
+of the structure menu.</p>
+<p><strong>Viewing the PDB Residue Numbering</strong><br>
+Sequences which have PDB entry or PDB file associations are annotated
+with sequence features from a group named with the associated PDB
+accession number or file name. Each feature gives the corresponding
+PDB Residue Number for each mapped residue in the seuqence. The
+display of these features is controlled through the
+<strong>"View→Sequence Features"</strong> menu item
+and the <a href="featuresettings.html">Feature Settings dialog
+box</a>.</p>
+</body>
+</html>
git://source.jalview.org / jalview.git / commitdiff