<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
<title>The Chimera PDB Viewer</title>
</head>
<body>
-<p><strong>The Chimera Viewer</strong></p>
-<p>Since Jalview 2.8.2, <a href="https://www.cgl.ucsf.edu/chimera/">Chimera</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). Chimera is available from the Jalview desktop, provided Chimera has been separately installed.</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).
-<p>The following menu entries are provided for viewing structure data<br>
+ <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/) 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). Chimera is
+ available from the Jalview desktop, provided Chimera has been
+ separately installed.
+ </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).
+ <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>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
currently selected sequence.<br /></li>
</ul>
<br>
-</p>
-<p><a name="align"><strong>Superposing structures based
-on their aligned sequences</strong></a><br>
-<p>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>
-<p>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. For comprehensive details of Chimera's commands, refer to the tool's Help menu.</p>
-<p>Basic screen operations (see <a href="https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/mouse.html">Chimera help</a> 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>
-</table>
-</p>
-<p><strong>Jalview Controls</strong>
-<p>The Jalview Chimera View window has up to five menus:
-<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>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></em></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>
+</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 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. For
+ comprehensive details of Chimera's commands, refer to the tool's
+ Help menu.
+ <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>
+ </em></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