</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
<!-- JAL-2005, JAL-599 -->Alignment sort by feature scores and feature counts preserves alignment ordering (and debugged for complex feature sets).
</li>
<li>
- <!-- -->
+ <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for viewing structures with Jalview 2.10
</li>
<li>
- <!-- JAL- -->
+ <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve genome, transcript CCDS and gene ids via the Ensembl and Ensembl Genomes REST API
+ </li>
+ <li>
+ <!-- JAL-2049 -->Protein sequence variant annotation computed for 'sequence_variant' annotation on CDS regions (Ensembl)
</li>
+ <li><!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot sequences</li>
<li>
<!-- JAL- -->
</li>
<ul>
<li><!-- JAL-2077 -->reinstate CTRL-click for opening pop-up menu on OSX</li>
<li><!-- JAL-2018-->Export features in Jalview format (again) includes graduated colourschemes</li>
- <li><!-- JAL-1722, JAL-2001-->More responsive when working with big alignments and lots of hidden columns</li>
+ <li><!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when working with big alignments and lots of hidden columns</li>
<li><!-- JAL-2053-->Hidden column markers not always rendered at right of alignment window</li>
<li><!-- JAL-2067 -->Tidied up links in help file table of contents</li>
<li><!-- JAL-2072 -->Feature based tree calculation not shown for DNA alignments</li>
</li>
<li><!-- JAL-1306 -->Quality and Conservation are now shown on load even when Consensus calculation is disabled</li>
<li>
- <!-- JAL- -->
+ <!-- -->
</li>
<li>
<!-- JAL- -->
<li><!-- JAL-2003 -->Export features should only export the currently displayed features for the current selection or view</li>
<li><!-- JAL-2036 -->Enable 'Get Cross-References' in menu after fetching cross-references</li>
<li><!-- JAL-2032 -->Mouseover of a copy of a sequence is not followed in the structure viewer</li>
- <li><!-- JAL-2163 -->Titles for individual alignments in splitframe not restored from project</li>
+ <li><!-- JAL-2163 -->Titles for individual alignments in splitframe not restored from project</li>
<li>
<!-- JAL-2145 -->missing autocalculated annotation at trailing end of protein alignment in transcript/product splitview when pad-gaps not enabled by default
</li>
</head>
<body>
<p>
- <strong>What's new ?</strong>
+ <strong>What's new in Jalview 2.10 ?</strong>
</p>
<p>
Jalview 2.10 is the next major release in the Jalview 2 series. Full
details are in the <a href="releases.html#Jalview.2.10.0">Jalview
2.10 Release Notes</a>, but the highlights are below.
</p>
- <p>
- <strong>Highlights in Jalview 2.10</strong>
<ul>
<li><strong>Ensembl sequence fetcher.</strong> Annotated Genes,
transcripts and proteins can be retrieved via Jalview's new <a
<li><strong>Import structures as mmCIF</strong>. Jalview
now downloads data from the EMBL-EBI's PDBe site as <a href="features/mmcif.html">mmCIF</a>.
This allows very large structures to be imported, such as the HIV virus capsid assembly.</li>
+ <li><strong>Chimera users will need to upgrade to
+ 1.11.1.</strong>If you use Chimera to view structures downloaded by
+ Jalview 2.10, you will need to make sure you are running the
+ latest version of <a href="features/chimera.html">Chimera</a>.</li>
</ul></li>
<li><strong>UniProt Free Text Search.</strong> The new search
dialog for UniProt allows you to browse and retrieve sequences
sequence. The reference sequence for alignment views can also be
saved and restored from Jalview projects.</li>
<li><strong>Ensembl and ENA 'show cross-references'
- support.</strong>The Calculations menu's 'Show cross-references' will now
+ support.</strong>The Calculations menu's <strong>'Show cross-references'</strong> will now
offer Ensembl as well as EMBLCDS and Uniprot when CDS/Protein
mapping data is available for download or display.</li>
+
</ul>
</body>
git://source.jalview.org / jalview.git / commitdiff