-
-
- <strong>Associating PDB files with Sequences</strong>
- <br> Discovery/Association of PDB entries to a sequence now
- happens automatically during the initialisation of the Structure
- Chooser Interface. Jalview uses the sequence's ID to query the PDB
- Rest API provided by the EBI to discover PDB Ids associated with the
- sequence.
-
- <br>
- <br>
- <strong>Configuring displayed meta-data for Structures</strong>
- <br> To configure the visible meta-data displayed for the
- discovered structures, click the 'Configure Displayed Columns' tab,
- then tick the options which you intend to make visible.
-
- <br>
- <br>
- <strong>Auto-selection of best Structures</strong>
- <br> Jalview can automatically filter and select the best
- structures using various metric categories avaialble from the
- meta-data of the structures. To perform this simply select any of the
- following options from the drop-down menu in the Structure Chooser
- interface: Best Uniprot coverage, Higest Resolution, Best Quality,
- Highest Protein Chain etc. When the 'Invert' option is selected,
- Jalview returns an inverse result for the current selected option in
- the drop-down menu.
+ <p>
+ <strong>Selecting and Viewing Structures</strong>
+ </p>
+ <p>The drop-down menu offers different options for structure
+ discovery; the 'Cached' view is shown automatically if existing
+ structure data has been imported for the selected sequences, and if
+ none is available, the import PDB/mmCIF file options are shown.</p>
+ <p>
+ Once one or more structures have been selected, pressing the <strong>View</strong>
+ or <strong>Add</strong> button will import them <a
+ href="viewingpdbs.html#afterviewbutton">a new or existing
+ structure view</a>. When multiple views are available, use the
+ drop-down menu to pick the target viewer for the structures.
+ </p>
+ <p>
+ <strong>Automated discovery of structure data</strong>
+ </p>
+ <p>
+ After selecting "3D Structure Data ..", Jalview queries 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 />
+ <p>
+ <strong><a name="cachedstructview">Viewing existing
+ structures for your sequences</a></strong>
+ </p>
+ <p>
+ If you have already loaded 3D structure data for the selected
+ sequences, the structure chooser will first open with the <strong>Cached
+ Structures View</strong>. This view shows associations between each
+ sequence, and chains for 3D structure files already in memory. If
+ you want to download additional structures, select one of the other
+ options from the drop down menu.
+ </p>
+ <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 '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
+ selected, structures are selected in reverse order for the current
+ criteria (e.g. worst quality rather than best).</p>