--- /dev/null
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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 Chimera PDB Viewer</title>
+</head>
+<body>
+ <p>
+ <strong>The Chimera Viewer</strong>
+ </p>
+ <p>
+ Since Jalview 2.8.2, <a href="http://www.cgl.ucsf.edu/chimera/">Chimera</a>
+ (http://www.cgl.ucsf.edu/chimera/) can be used for viewing
+ structures opened via the <a href="structurechooser.html"><strong>"View
+ Structure Data.."</strong> dialog</a>.
+ </p>
+ <p>
+ You can set a default choice of Jmol or Chimera structure viewer in
+ <a href="preferences.html#structure"> Preferences</a>. You can also
+ optionally specify the path to the Chimera program here (if it
+ differs from the standard paths searched by Jalview).<br /> <strong>Please
+ make sure your version of Chimera is up to date. Jalview requires
+ at least Chimera version 1.11.1</strong>
+ </p>
+ <p>
+ If you save your Jalview session as a project file, the state of any
+ open Chimera windows will also be saved, and can be reopened by
+ loading the project file on any machine with Chimera installed. <em>Since
+ Jalview 2.9.</em>
+ <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 Chimera 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>Chimera→Align</em></a> menu option
+ from the menu bar of the structure view window to superpose the
+ structures using the updated alignment.<br>
+ </p>
+ <p>
+ <strong>Chimera 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 ([RES]Num:Chain). Moving the mouse over an
+ associated residue in an alignment window highlights the associated
+ atoms in the displayed structures. When residues are selected in the
+ Chimera window, they are highlighted on the alignment.
+ <p>For comprehensive details of Chimera's commands, refer to the
+ tool's Help menu.</p>
+ <p>
+ <strong>Selecting residues in Jalview from Chimera</strong><br />
+ When a selection is highlighted in a Jalview window, use the
+ <em>Select→Select Highlighted Region</em> or press <em>B</em>
+ to add the mapped positions to the alignment window's column
+ selection.<br /> <em>Hint: Use your machine's 'switch
+ application' key combination (Alt-Tab on Windows and Linux,
+ Cmd-Tab on OSX) to quickly switch between UCSF Chimera and Jalview
+ before pressing 'B' to select highlighted regions.</em>
+ </p>
+ <p>
+ Basic screen operations (see <a
+ href="http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/mouse.html">Chimera
+ help</a> at
+ http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/mouse.html
+ for full details).
+ <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>Left Click and Drag</td>
+ </tr>
+ <tr>
+ <td>Zoom</td>
+ <td>Right Click<br> drag mouse up or down
+ </td>
+ <td>Right Click<br>drag mouse up or down
+ </td>
+ <td>cmd or Right + Click and drag mouse up or down, <br>or
+ use mouse scroll button
+ </td>
+ </tr>
+ <tr>
+ <td>Move Origin</td>
+ <td>Middle Button + Drag</td>
+ <td>Middle Button and drag</td>
+ <td>alt + Click<br> and drag
+ </td>
+ </tr>
+ <tr>
+ <td>Select Residues</td>
+ <td>Ctrl + Click (and drag to select a region)</td>
+ <td>Ctrl + Click (and drag)</td>
+ <td>Ctrl + Click (and drag)</td>
+ </tr>
+ </table>
+ </p>
+ <p>
+ <strong>Jalview Controls</strong>
+ <p>The Jalview Chimera View window has up to five menus:</p>
+ <ul>
+ <li><Strong>File<br>
+ </strong>
+ <ul>
+ <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 (if more than
+ one) 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>Uses the Chimera 'rainbow chain' command to apply a
+ different colour to each chain.</em></li>
+ <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 Chimera<br></strong><em>Defers
+ any colouring operations to Chimera. Select this if you want
+ to use the Chimera 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>Chimera<br>
+ </strong><em>This pulldown menu is only displayed if there are multiple
+ structures shown in the Chimera 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 />
+ <br />
+ </em></li>
+ <li><a name="annotxfer"><strong>Write Jalview
+ features</strong></a><br /> <em>Selecting this option will create
+ new residue attributes for any features currently visible in
+ the associated alignment views, allowing those positions to
+ be selected and analysed with via Chimera's 'Render by
+ Attribute' tool (found in the Tools submenu called Structure
+ Analysis).<br /> <br />If you use this option, please
+ remember to select the <em>Refresh Menus</em> option in
+ Chimera's Render by Attribute dialog box in order to see the
+ attributes derived from Jalview sequence features.
+ </em></li>
+ <li><strong>Fetch Chimera Attributes</strong><br /> <em>This
+ submenu lists available Chimera residue attributes that can
+ be imported as Jalview features on associated sequences.<br />This
+ is particularly useful for transferring quantitative
+ positional annotation. For example, structure similarity for
+ an alignment can be visualised by transferring the local
+ RMSD attributes generated by Chimera's Match->Align tool
+ onto aligned sequences and displayed with a <a
+ href="featureschemes.html">Graduated feature colour
+ scheme</a>. </li>
+ </ul></li>
+ <li><strong>Help<br>
+ </strong>
+ <ul>
+ <li><strong>Chimera Help<br>
+ </strong><em>Access the Chimera Help documentation in a new browser
+ window.</em></li>
+ </ul></li>
+ </ul>
+ <p>
+ <strong>Chimera and Windows Firewall</strong>
+ </p>
+ Jalview and Chimera communicate using Chimera's
+ <a
+ href="http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/restserver/restserver.html">REST
+ service</a>
+ (http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/restserver/restserver.html).
+ <br> Technically this requires both Chimera and Jalview to open
+ ports on the local network, and this may be blocked by Windows
+ Firewall with a warning message such as
+ <br /> "Windows Firewall has blocked some features of this program"
+ (where the program may be jp2launcher.exe for Jalview Webstart, or
+ java.exe or javaw.exe for the InstallAnywhere version).
+ <br /> To allow Jalview and Chimera to interact, you may need to add
+ permission for the program to communicate over the network. This can
+ be done from the warning dialogue, or in Control Panel, Firewall
+ settings.
+</body>
+</html>
git://source.jalview.org / jalview.git / blobdiff