+++ /dev/null
-<html>
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * 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
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- * 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>