-<html>\r
-<!--\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview is free software: you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License \r
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * 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></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
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<head>
+<title>The Jmol PDB Viewer</title>
+</head>
+<body>
+ <p>
+ <strong>The Jmol PDB Viewer</strong>
+ </p>
+ <p>
+ Since Jalview 2.3, <a href="http://jmol.sourceforge.net/">Jmol</a>
+ has been integrated into Jalview for interactively viewing
+ structures opened by entries in the <strong>"Structure"</strong>
+ submenu in the <a href="../menus/popupMenu.html">sequence id
+ pop-up menu</a> (if you can't see this, then you need to <a
+ href="viewingpdbs.html"
+ >associate a PDB structure</a> with the sequence). Jmol is available
+ from the Jalview desktop and should also run in the JalviewLite
+ applet, providing the browser supports Java 1.5. If Jmol is not
+ available, then the original <a href="pdbviewer.html">internal
+ pdb viewer</a> will be used as a fallback.
+ </p>
+ <!-- <p>The following menu entries are provided for viewing structure data<br>
+ <ul>
+ <li>The <strong>"Structure→View
+ Structure→</strong> submenu allows a single PDB structure to be chosen
+ for display from the available structures for a sequence.
+ </li>
+ <li>The <strong>"Structure→View all <em>N</em>
+ structures
+ </strong> option will open a new window containing all structures associated
+ with the current selection.
+ </li>
+ <li>The <strong>"Structure→View all <em>N</em>
+ representative structures
+ </strong> option will open a new window containing exactly one structure per
+ currently selected sequence.<br />
+ <em>The View representative structures option was introduced in
+ Jalview 2.8.1</em></li>
+ </ul>
+ <br>
+</p> -->
+ <p>
+ <a name="align"><strong>Superposing structures based on
+ their aligned sequences</strong></a><br> If several structures are
+ available on the alignment, you may add additional structures to an
+ existing Jmol view by selecting their entry in the appropriate
+ pop-up menu. Jalview will ask you if you wish to add the structure
+ to the existing alignment, and if you do, it will import and
+ superimpose the new PDB file using the corresponding positions from
+ the alignment. If the alignment is subsequently edited, you can use
+ the <a href="#sAlign"><em>Jmol→Align</em></a> menu option from
+ the menu bar of the structure view window to superpose the
+ structures using the updated alignment.<br> <em>Sequence
+ based structure superposition was added in Jalview 2.6</em>
+ </p>
+ <p>
+ <strong>Controls</strong><br> The structure is by default
+ rendered as a ribbon diagram. Moving the mouse over the structure
+ brings up tooltips giving the residue name, PDB residue number and
+ chain code, atom name and number
+ ([RES]Num:Chain.AtomName#AtomNumber). If a mapping exists to a
+ residue in any associated sequences, then this will be highlighted
+ in each one's alignment window. The converse also occurs - moving
+ the mouse over an associated residue in an alignment window
+ highlights the associated atoms in the displayed structures.
+ </p>
+ <p>Selecting a residue highlights its associated sequence residue
+ and alpha carbon location. Double clicking an atom allows distances
+ to be measured from it to any other atom in the structure.</p>
+ <p>
+ <table border="1">
+ <tr>
+ <td><strong>Action</strong></td>
+ <td><strong>Windows</strong></td>
+ <td><strong>Unix</strong></td>
+ <td><strong>Mac/OSX</strong></td>
+ </tr>
+ <tr>
+ <td>Rotate View</td>
+ <td>Left Click and Drag</td>
+ <td>Left Click and Drag</td>
+ <td>Click and Drag</td>
+ </tr>
+ <tr>
+ <td>Zoom</td>
+ <td>Shift + Left Click<br> drag mouse up or down
+ </td>
+ <td>Shift + Left Click<br> or middle button<br>
+ drag mouse up or down
+ </td>
+ <td>Left-Alt + Click and drag mouse up or down</td>
+ </tr>
+ <tr>
+ <td>Select/<br> Deselect<br> Residue
+ </td>
+ <td>Left Click</td>
+ <td>Left Click</td>
+ <td>Click</td>
+ </tr>
+ <tr>
+ <td>Roll View</td>
+ <td>Shift + Left Click<br> drag mouse to left or right
+ </td>
+ <td>Shift + Left Click<br> or middle button<br>
+ drag mouse to left or right
+ </td>
+ <td>Left-Alt + Click and drag mouse to left or right</td>
+ </tr>
+ <tr>
+ <td>Move Origin</td>
+ <td>Shift+Control+Left Click<br> or Middle Button<br>
+ + Drag
+ </td>
+ <td>Middle-Button<br> and<br> drag
+ </td>
+ <td>Shift+Control+Left Click<br> or Middle Button<br>
+ and drag
+ </td>
+ </tr>
+ <tr>
+ <td>Jmol Menu</td>
+ <td>Right-Click</td>
+ <td>Right-Click</td>
+ <td>Apple-Click</td>
+ </tr>
+ </table>
+ </p>
+ <p>The window has up to five menus:
+ <ul>
+ <li><Strong>File<br>
+ </strong>
+ <ul>
+ <li><strong>Save As<br>
+ </strong><em>Save the displayed PDB File, or the current view as an
+ EPS or PNG file.</em></li>
+ <li><strong>View Mapping<br>
+ </strong><em> Opens a text window showing the alignment between the
+ residues corresponding to alpha-carbon atoms in the PDB
+ structure and the residues in the associated sequence.</em></li>
+ </ul></li>
+ <li><strong>View</strong>
+ <ul>
+ <li><strong>Show Chains<br>
+ </strong><em>Select which of the PDB file's chains are to be
+ displayed.</em></li>
+ <li><strong>Colour by ..<br></strong><em>Submenu
+ allowing specific alignment views to be selected for
+ colouring associated chains in the structure display. This
+ menu contains all the alignment views associated with the
+ structure view, with those used to colour the view indicated
+ by ticks. Addditionally, it contains the following menu
+ entries:</em>
+ <ul>
+ <li><strong>Select many views<br></strong><em>When
+ this option is enabled, selecting an alignment view adds
+ it to the set used to colour the structures. Use this
+ when colouring structures related to a number of
+ alignments involving different domains or chains which
+ are shown in the same structure view.</em></li>
+ <li><strong>Select all views<br></strong><em>This
+ is only enabled when </em><strong>Select many views</strong><em>
+ is also enabled, and will add all associated views to
+ the set used to colour the structure display.</em></li>
+ <li><strong>Invert selection<br></strong><em>This
+ is only enabled when </em><strong>Select many views</strong><em>
+ is also enabled, and will replace the current set of
+ views with any remaining views not currently used to
+ colour the structure display.</em></li>
+ </ul></li>
+ </ul>
+ <li><strong>Colours<br>
+ </strong>
+ <ul>
+ <li><strong>By Sequence<br>
+ </strong><em> Colours each residue in the structure with the colour
+ of its corresponding residue in the associated sequence as
+ rendered in the associated alignment views, including any
+ Uniprot sequence features or region colourings.<br />Pick
+ which of the associated alignment views are used to colour
+ the structures using the <strong>View→Colour
+ by ..</strong> sub menu.
+ </em><br> Residues which only exist in the PDB structure are
+ coloured white if they are insertions (relative to the
+ associated sequence in the alignment) and grey if they are N
+ or C terminal flanks outside the region mapped to the
+ alignment window's sequence.</em></li>
+ <li><strong>By Chain<br>
+ </strong><em> Assigns a random colour to each PDB chain.</em>
+ <li><strong>Charge & Cysteine<br>
+ </strong><em> Highlights cysteines in yellow, anionic (Aspartic Acid
+ or Glutamic Acid) residues in red, and cationic (Lysine or
+ Arginine) residues in blue.</em></li>
+ <li><strong>Colour with Jmol<br></strong><em>Defers
+ any colouring operations to Jmol. Select this if you want to
+ use the Jmol scripting interface or menu to modify the view
+ directly.</em></li>
+ <li><strong>Standard and User Defined Jalview
+ colourschemes.<br>
+ </strong><em>The remaining entries apply the colourschemes available
+ from the standard and user defined <a
+ href="../colourSchemes/index.html"
+ >amino acid colours</a>.
+ </em></li>
+ </ul></li>
+ <li><strong>Jmol<br>
+ </strong><em>This pulldown menu is only displayed if there are multiple
+ structures shown in the Jmol window, and Jalview can also locate
+ at least two of the structures in the currently associated
+ alignment view.</em>
+ <ul>
+ <li><strong><a name="sAlign">Align</a> <br> </strong><em>
+ When selected, the associated alignment will be used to
+ superimpose all the structures in the view onto the first
+ structure in the alignment. The regions used to calculate
+ the superposition will be highlighted using the 'Cartoon'
+ rendering style, and the remaining data shown as a chain
+ trace.<br> (This option was introduced in Jalview 2.6)
+ </em></li>
+ </ul></li>
+ <li><strong>Help<br>
+ </strong>
+ <ul>
+ <li><strong>Jmol Help<br>
+ </strong><em>Access the Jmol Help documentation in a new browser
+ window.</em></li>
+ </ul></li>
+ </ul>
+ </p>
+ <p>
+ <strong>Functionality provided by Jmol</strong>
+ </p>
+ <p>Jmol's own functions are accessed by clicking the 'Jmol' logo
+ or right-clicking in the structure display area. Either way will
+ open the Jmol pop-up menu, which provides access to a number of
+ features for controlling the colour and display of molecules, adding
+ measurements and labels, plotting surfaces, and display animation.
+ The 'Set Picking' menu controls the behaviour of single and double
+ mouse clicking on the structure, and the 'Console' option opens the
+ Jmol scripting console.</p>
+ <p>
+ The state of each Jmol display is stored within <a
+ href="jalarchive.html"
+ >Jalview archives</a> as a Jmol state recovery script file. This means
+ that any Jmol visualization effects that you add beyond those
+ provided by Jalview will be able to be stored and recovered along
+ with the displayed alignments in Jalview.
+ </p>
+ <p>
+ <strong>More Information</strong>
+ </p>
+ <p>
+ Jmol is a sophisticated program in its own right, with its own
+ command console and scripting language. Only the essentials have
+ been described here - the interested reader is referred to <a
+ href="http://jmol.sourceforge.net/docs/"
+ >Jmol's own comprehensive online documentation</a>.
+ </p>
+ </p>
+</body>
+</html>
git://source.jalview.org / jalview.git / blobdiff