(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>. In Jalview 2.11.2, support
- was also added for ChimeraX.
+ was also added for ChimeraX, and <a href="pymol.html">Pymol</a>.
</p>
<p>
You can set a default choice of Jmol or Chimera structure viewer in
<p>
<strong>Jalview requires Pymol V 2.5.0 (community edition)
or later</strong> <br />Jalview requires Pymol's RPC interface, which is
- not available in older versions of the Pymol community edition.
+ not available in older versions of the Pymol community edition.
</p>
<p>
<strong>Known Limitations</strong><br />
properties or highlighting sequence regions corresponding to
structure selections or mouse-overs in Pymol.</li>
<li>Jalview to Pymol communication currently doesn't highlight
- the positions on structures corresponging to moused over residues
+ the positions on structures corresponding to moused-overs
in Jalview.</li>
</ul>
<p>
<strong>Selection of the best structure for each sequence</strong>
</p>
<p>Jalview can automatically select the best structures according
- to meta-data provided by the PDB. For alignments with no existing
- structure data, the 'PDBe Best Quality' structure for each sequence will
- by default be selected, but clicking on the drop down menu allows
- other criteria to be chosen, including Resolution (only defined for
- X-Ray structures), Highest Protein Chain etc. When 'Invert' is
+ to meta-data provided by the search service. The 'PDBe Best Quality' structure for each sequence will
+ by default be selected when no other structure data is available. If 3D-models from other sources are also available, then 'Best 3D Beacons coverage' will be show.
+ <br/><br/>Clicking on the drop down menu allows
+ other criteria to be chosen. For the PDBe, these include including Resolution (only defined for
+ X-Ray structures), Highest Protein Chain etc. When 3D-Beacons results are available, structures can be selected based on their specific provider, or by their coverage of the aligned sequences.<br/>
+ <br/>When 'Invert' is
selected, structures are selected in reverse order for the current
criteria (e.g. worst quality rather than best).</p>
<p>
- <img src="schooser_main.png" style="width: 499px; height: 437px;">
+ <img src="schooser_main.png" style="width: 820px; height: 458px;">
<!-- <p><img src="schooser_config.png" style="width: 463px; height: 369px; ">
<p><img src="schooser_drop-down.png" style="width: 464px; height: 368px; ">
<p><img src="schooser_enter-id.png" style="width: 467px; height: 373px; ">
<br/>
The 3D-Beacons Network search requires UniProt references and Jalview will ask
to attempt to fetch these references for the selected sequences.
- UniProt references might not always be found in which case you can revert to the PDB
- search.
+ If no UniProt references are found, Jalview will still search the PDB for potential matches for the sequence's ID string.
<br/>
<img src="3dbeacons_structurechooser.png"/>
<br/>
- If structures are found through the 3D-Beacons network you can filter which structures
- are shown using the drop-down filter at the top of the Structure Chooser window.
- <br/>
+ Structures found through the 3D-Beacons network can be filtered using the drop-down filter at the top of the Structure Chooser window.
You can view information about each related model, such as the resource providing
- each model, in the columns displayed. You can sort the list of models by clicking on
+ each model, in the displayed columns, and models can be reordered by clicking on
column headings.
<br/>
Select and view the structures in the usual way using the <a href="viewingpdbs.html#afterviewbutton">open structure options</a> at
</p>
<p>Information on each structure available is displayed in columns
in the dialog box. By default, only the title, resolution and PDB
- identifier are shown, but many more are provided by the PDBe. To
- configure which ones are displayed, select the 'Configure Displayed
- Columns' tab and tick the columns which you want to see.</p>
+ identifier are shown, but many more are provided by the PDBe.
+ 3D-Beacons structures have different data, including a quality score
+ (such as Qmeans_DISCO). To configure which ones are displayed,
+ select the 'Configure Displayed Columns' tab and tick the columns
+ which you want to see.</p>
<p>
<img src="schooser_enter-id.png"
- style="width: 464px; height: 173px;">
- <br/>
- <strong>Manual selection/association of PDB files with
- Sequences</strong>
+ style="width: 464px; height: 173px;"> <br /> <strong>Manual
+ selection/association of PDB files with Sequences</strong>
</p>
<p>To manually associate PDB files with a sequence, select 'From
File', or 'Enter PDB Id' from the drop-down menu:
<td align="left" valign="top">
<ul>
<li>
- <!-- -->
+ <!-- JAL- -->
+ </li>
+ <li>
+ <!-- JAL-3863 -->Support for Canonical Uniprot IDs
</li>
</ul> <em>JalviewJS</em>
<ul><li><!-- 3624 -->PDB structures mapped to Uniprot Sequences with SIFTS</li>
<li><!-- JAL-2848 -->Cancel from Amend Features doesn't reset a modified graduated colour</li>
</ul> <em>Development</em>
<ul>
- <li>Fixed non-fatal gradle errors during build</li>
+ <li>Gradle<ul><li>Fixed non-fatal gradle errors during build</li>
+ <li><!-- JAL-3745 -->Updated build.gradle for use with Gradle v.6.6+</li></ul></li>
</ul>
</td>
<p>
<strong>Highlights in 2.11.2</strong>
</p>
- <p><strong>New features for working with 3D Structure</strong><br/>
- Jalview 2.11.2 features a number of new capabilities:<ul><li><strong>Linked viewing with <em>ChimeraX</em> and <em>PyMol</em></strong><br/>Simply configure your prefered viewer for 3D molecular data in <a href="features/preferences.html#structure">Jalview's structure preferences</a>, make sure that Jalview can locate the viewer's installation, and open a new view via the 3D Structure Chooser!</li>
- <li><strong>View predicted protein structures via 3D-Beacons</strong><br/>
- Jalview 2.11.2's <a href="features/structurechooser.html">Structure Chooser includes a client for the 3D-Beacons Network</a>, a new service that allows predicted and observed 3D models for proteins in Uniprot from a range of resources, including AlphaFold DB, SWISS-MODEL and a growing number of other resources.
- </li>
- <p><strong>Retrieval
- </p>
- <p>
- For the full release notes, see <a
- href="releases.html#Jalview.2.11.1.4">the Jalview 2.11.1.4
- release notes</a>.
- </p>
<p>
- <strong>Known Issues</strong>
- </p>
- <p>New known issues in this release affect recovery of CDS/Protein
- relationships from project files, and interactive selection of
- protein sequences from a tree built on linked nucleotide sequences.
- We will provide patches for these issues as soon as possible.</p>
+ <strong>New features for working with 3D Structure</strong><br />
+ Jalview 2.11.2 features a number of new capabilities:
+
+ <ul>
+ <li><strong>Linked viewing with <em>ChimeraX</em> and
+ <em>PyMol</em></strong><br />Simply configure your prefered viewer for 3D
+ molecular data in <a href="features/preferences.html#structure">Jalview's
+ structure preferences</a>, make sure that Jalview can locate the
+ viewer's installation, and open a new view via the 3D Structure
+ Chooser!</li>
+ <li><strong>View predicted protein structures via
+ 3D-Beacons</strong><br /> Jalview 2.11.2's <a
+ href="features/structurechooser.html">Structure Chooser
+ includes a client for the 3D-Beacons Network</a>, a new service that
+ allows predicted and observed 3D models for proteins in Uniprot
+ from a range of resources, including AlphaFold DB, SWISS-MODEL and
+ a growing number of other resources.</li>
+ <p>
+ <strong>Retrieval of 3D models via 3D-Beacons</strong> <br>The
+ 3D-Beacons network (<a
+ href="https://www.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/">www.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/</a>)
+ provides a central point for the retrieval of predicted and
+ observed 3D structures for sequences in Uniprot, including
+ homology models from Swiss-model and deep learning based
+ predictions from the EBI's Alphafold database (Orengo et al. 2020,
+ <a href="https://doi.org/10.12688/f1000research.20559.1">doi:10.12688/f1000research.20559.1</a>).<br>
+ See the <a href="features/structurechooser.html">Structure
+ Chooser's documentation</a>.
+ </p>
+ <p>
+ <strong>Support for viewing structures with ChimeraX and
+ Pymol</strong><br> Structures Preferences tab provides new options
+ allowing ChimeraX and Pymol to be used for visualising external 3D
+ structures. Jalview 2.11.2 has been tested with Pymol 2.5.0
+ (community) and 2.5.2 (incentive). For ChimeraX, we recommend
+ using v1.3 or later. Jalview's 3D structure viewer system has been
+ re-architected to allow easier integration of external structure
+ viewers, and takes advantage of the strucViz2 Chimera
+ communications library developed by Scooter Morris (<a
+ href="https://doi.org/10.1093/bioinformatics/btm329">doi:10.1093/bioinformatics/btm329</a>).
+ </p>
+ <p>
+ For the full release notes, see <a
+ href="releases.html#Jalview.2.11.1.4">the Jalview 2.11.1.4
+ release notes</a>.
+ </p>
+ <p>
+ <strong>Known Issues</strong>
+ </p>
+ <p>New known issues in this release affect recovery of
+ CDS/Protein relationships from project files, and interactive
+ selection of protein sequences from a tree built on linked
+ nucleotide sequences. We will provide patches for these issues as
+ soon as possible.</p>
</ul>
</body>
</html>
git://source.jalview.org / jalview.git / commitdiff