* \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 Jmol PDB Viewer</title>\r
+</head>\r
+<body>\r
+<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
+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
+sequence). Jmol is available from the Jalview desktop and should also\r
+run in the JalviewLite applet, providing the browser supports Java 1.5.\r
+If Jmol is not available, then the original <a href="pdbviewer.html">internal\r
+pdb viewer</a> will be used as a fallback.</p>\r
+<p><a name="align"><strong>Superposing structures based\r
+on their aligned sequences</strong></a><br>\r
+If several structures are available on the alignment, you may add\r
+additional structures to an existing Jmol view by selecting their entry\r
+in the appropriate pop-up menu. Jalview will ask you if you wish to add\r
+the structure to the existing alignment, and if you do, it will import\r
+and superimpose the new PDB file using the corresponding positions from\r
+the alignment. If the alignment is subsequently edited, you can use the\r
+<a href="#sAlign"><em>Jmol→Align</em></a> menu option from the\r
+menu bar of the structure view window to superpose the structures using\r
+the updated alignment.<br>\r
+<em>Sequence based structure superposition was added in Jalview 2.6</em>\r
+</p>\r
+<p><strong>Controls</strong><br>\r
+The structure is by default rendered as a ribbon diagram. Moving the\r
+mouse over the structure brings up tooltips giving the residue name, PDB\r
+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 one's\r
+alignment window. The converse also occurs - moving the mouse over an\r
+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>\r
+ drag mouse up or down</td>\r
+ <td>Shift + Left Click<br>\r
+ or middle button<br>\r
+ drag 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>\r
+ drag mouse to left or right</td>\r
+ <td>Shift + Left Click<br>\r
+ or middle button<br>\r
+ 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>\r
+ or Middle Button<br>\r
+ + Drag</td>\r
+ <td>Middle-Button<br>\r
+ and<br>\r
+ drag</td>\r
+ <td>Shift+Control+Left Click<br>\r
+ 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 up to five 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\r
+ 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>\r
+ </strong><em>Select which of the PDB file's chains are to be displayed.</em></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\r
+ the standard and user defined <a href="../colourSchemes/index.html">amino\r
+ acid colours</a>.</em></li>\r
+ </ul>\r
+ </li>\r
+ <li><strong>Jmol<br>\r
+ </strong><em>This pulldown menu is only displayed if there are multiple\r
+ structures shown in the Jmol window, and Jalview can also locate at\r
+ least two of the structures in the currently associated alignment view.</em>\r
+ <ul>\r
+ <li><strong><a name="sAlign">Align</a> <br>\r
+ </strong><em> When selected, the associated alignment will be used to\r
+ superimpose all the structures in the view onto the first structure in\r
+ the alignment. The regions used to calculate the superposition will be\r
+ highlighted using the 'Cartoon' rendering style, and the remaining\r
+ data shown as a chain trace.<br>\r
+ (This option was introduced in Jalview 2.6)</em></li>\r
+ </ul>\r
+ </li>\r
+ <li><strong>Help<br>\r
+ </strong>\r
+ <ul>\r
+ <li><strong>Jmol Help<br>\r
+ </strong><em>Access the Jmol Help documentation in a new browser window.</em></li>\r
+ </ul>\r
+ </li>\r
+</ul>\r
+</p>\r
+<p><strong>Functionality provided by Jmol</strong></p>\r
+<p>Jmol's own functions are accessed by clicking the 'Jmol' logo or\r
+right-clicking in the structure display area. Either way will open the\r
+Jmol pop-up menu, which 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' menu\r
+controls the behaviour of single and double mouse clicking on the\r
+structure, and the 'Console' option opens the Jmol scripting console.</p>\r
+<p>The state of each Jmol display is stored within <a\r
+ href="jalarchive.html">jalview archives</a> as a Jmol state recovery\r
+script file. This means that any Jmol visualization effects that you add\r
+beyond those provided by Jalview will be able to be stored and recovered\r
+along with the displayed alignments in Jalview.</p>\r
+<p><strong>More Information</strong></p>\r
+<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 <a\r
+ href="http://jmol.sourceforge.net/docs/">Jmol's own comprehensive\r
+online documentation</a>.</p>\r
+</p>\r
+</body>\r
+</html>\r
git://source.jalview.org / jalview.git / blobdiff