<strong>Automated discovery of structure data</strong>
</p>
<p>
- After selecting "3D Structure Data ..", Jalview queries the PDB via
+ After selecting "3D Structure Data ..", Jalview queries its available structure data providers. When Uniprot identifiers are available, it queries the <a href="#3dbeaconssearch">3D-Beacons network</a> (since Jalview 2.11.2), otherwise it searches the PDB via
the PDBe SOLR Rest API provided by EMBL-EBI to discover PDB IDs
associated with the sequence. It does this based on the sequence's
ID string, and any other associated database IDs. <br />
- <br />
- Since Jalview 2.11.2, you can also <a href="#3dbeaconssearch">initiate a search
- of the 3D-Beacons Network</a>.
</p>
<p>
<strong><a name="cachedstructview">Viewing existing
<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; ">
<strong><a name="3dbeaconssearch">3D-Beacons Network Search</a></strong>
</p>
<p>
- To initiate a search of the 3D-Beacons Network—which searches
- across experimentally determined and predicted structure models from
- several resources including PDBe, AlphaFold DB, SWISS-MODEL, PED, SASDB, Genome3D and
- PDBe-KB—click on the <strong>3D-Beacons Search</strong> button at the top of the
- Structure Chooser window.
- <br/>
- <img src="3dbeacons_button.png"/>
- <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.
- <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/>
- 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
- column headings.
- <br/>
- Select and view the structures in the usual way using the <a href="viewingpdbs.html#afterviewbutton">open structure options</a> at
- the bottom of the Structure Chooser window.
+ 3D beacons searches across experimentally determined and predicted
+ structure models from several resources including PDBe, AlphaFold
+ DB, SWISS-MODEL, PED, SASDB, Genome3D and PDBe-KB.<br /> If your
+ sequences have Uniprot identifiers, Jalview will query the
+ 3D-Beacons network to discover relevant 3D structures and models.
+ When no uniprot identifiers are available you can initiate Uniprot
+ identifier discovery and a subsequent search of the 3D-Beacons
+ Network by pressing the <strong>3D-Beacons Search</strong> button at
+ the top of the Structure Chooser window. <br /> <img
+ src="3dbeacons_button.png" /> <br />When the search button is
+ pressed, Jalview will ask to attempt to fetch any additional uniprot
+ references for the selected sequences - we do this because fetching
+ large numbers of Uniprot references can take some time. For
+ sequences without Uniprot accessions, Jalview will still search the
+ PDB for potential matches for the sequence's ID string. <br />
+ <br /> <img src="3dbeacons_structurechooser.png" /> <br /> <br />
+ 3D Beacons provides some additional information for each model,
+ including what positions on the Uniprot sequence have structure
+ data. These metadata (described below) are shown in the columns of
+ the table and used to provide additional filter options.<br />Use
+ the drop-down filter menu and table to browse and select structures,
+ and finally view them using the
+ <a href="viewingpdbs.html#afterviewbutton">open structure
+ options</a> at the bottom of the Structure Chooser window.
</p>
+ <strong>Options for selecting structures from 3D Beacons</strong><br />
+ Structures found through the 3D-Beacons network can be filtered
+ using the drop-down filter at the top of the Structure Chooser
+ window. The options usually available are:
+
+ <ul>
+ <li><strong>Best 3D Beacons Coverage</strong> - selects one
+ structure for each sequence from available structures those that
+ are the highest quality (ie experimental structures, or highly
+ accurate predictions) and cover the most number of residues in the
+ alignment.</li>
+ <li><strong>3DB Provider - ...</strong> selects the best
+ quality structure for each sequence provided by a specific source
+ (e.g. PDB, EBI-AlphaFold, SwissModel).</li>
+ <li><strong>Multiple 3D-Beacons Coverage</strong> - employs a
+ heuristic to identify structures providing the best quality
+ structure data for every position in each sequence.<br /> <em>Note:
+ structure superpositions may fail when this option is used
+ because the best covering structure set for a sequence often do
+ not overlap.</em></li>
+ </ul>
+
<p>
<strong>Exploration of meta-data for available structures</strong>
</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>
- </p>
- <p>To manually associate PDB files with a sequence, select 'From
- File', or 'Enter PDB Id' from the drop-down menu:
- <ul>
- <li><strong>From File</strong> - allows you to load a PDB file
- from the local machine or network and associate it with the
- selected sequence. PDB files associated in this way will also be
- saved in the <a href="jalarchive.html">Jalview Archive file</a>.<br></li>
- <li><strong>Enter PDB Id</strong> - allows you specify a PDB ID
- for your sequence. The PDB Rest API, provided by EMBL-EBI, is used
- to validate and fetch structure data.<br></li>
- </ul>
-
- <p>
- <em>The Structure Chooser interface was introduced in Jalview
- 2.9. </em>
+ style="width: 464px; height: 173px;"> <br /> <strong>Manual
+ selection/association of PDB files with Sequences</strong>
</p>
+ <p>
+ <strong>Manual Association of PDBe accessions with sequences</strong>
+ </p>
+ <p>If for some reason the PDBe and 3D beacons search fail to
+ automatically the PDB structure or model you wish to import, you can
+ select 'Enter PDB Id' from the drop-down menu to manually specify PDB
+ identifiers for one or more selected sequences. The PDB Rest API,
+ provided by EMBL-EBI, is used to validate accessions exist, and fetch
+ structure data.</p>
+ <p>
+ <strong><a name="loadpdbfromfile">Import structure models
+ and metadata from file</a></strong>
+ </p>
+ <p>
+ Selecting the <strong>From File</strong> option from the drop down
+ menu allows 3D structure data to be imported from your own computer.
+ PDB or mmCIF files associated in this way are also saved in <a
+ href="jalarchive.html">Jalview Projects</a>. <br /> <img
+ src="local-pdb-import.png" style="width: 496px; height: 482px;"><br />
+ The 'From File' dialog provides a drop down menu which allows you to
+ specify how the Temperature Factor metadata for each residue in the 3D
+ structure data file is interpreted:
+
+ <ul>
+ <li>Default - Jalview will try to automatically determine whether
+ to show as 'Temperature Factor', 'AlphaFold Reliability' or 'Model
+ Quality'</li>
+ <li>PLDDT - Model has PLDDT scores in the temperature factor
+ column.</li>
+ </ul>
+ <p>
+ An additional <em>Predicted Alignment Error</em> file can also be
+ provided when importing 3D structure data. Jalview supports import of
+ PAE Matrices provided as <a href="../io/paematrixformat.html">AlphaFold
+ format JSON files</a> - which are also produced by ColabFold. See <a
+ href="paematrices.html">Working with PAE Matrices</a> for details on
+ what Jalview allows you to do with associated PAE matrix data.
+ </p>
+ <p>
+ <em>The Structure Chooser interface was introduced in Jalview
+ 2.9. </em>
+ </p>
</body>
</html>