</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.
+ (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).
+ 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>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 /></li>
- </ul>
- <br>
-</p> -->
<p>
<a name="align"><strong>Superposing structures based on
their aligned sequences</strong></a><br> If several structures are
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.
+ 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
+ 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">
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>.
+ href="../colourSchemes/index.html">amino acid
+ colours</a>.
</em></li>
</ul></li>
<li><strong>Chimera<br>
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>
+ trace.<br/><br/>
</em></li>
- </ul></li>
- <li><strong>Help<br>
+ <li><strong><a name="experimental">EXPERIMENTAL FEATURES</a></strong><br/>
+ <em>
+ These are only available if the <strong>Tools→Enable
+ Experimental Features</strong> option is enabled. (Since Jalview 2.10.2)</em>
+ <ul>
+ <li><strong>Write Jalview features</strong><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><br />
+ <a href="https://issues.jalview.org/browse/JAL-2295">View
+ this function's issue in Jalview's bug tracker</a></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>.
+ </em><a href="https://issues.jalview.org/browse/JAL-2296">View
+ this function's issue in Jalview's bug tracker</a></li>
+ </ul></li>
+ <li><strong>Help<br>
</strong>
<ul>
<li><strong>Chimera Help<br>
</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>
+ 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
git://source.jalview.org / jalview.git / blobdiff