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-<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>
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