* PURPOSE. See the GNU General Public License for more details.\r
* \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>\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> as a jmol state recovery script\r
+file. 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
git://source.jalview.org / jalview.git / blobdiff