* 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
+-->\r
git://source.jalview.org / jalview.git / blobdiff