X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fstructurechooser.html;h=fc71826be1417e1c0fceb82dd17a5504fa2eea47;hb=25cf211cb3675e40e438c3dc0267806e3f1d461c;hp=b276897cbdeb549585ede93ac809a683457ac6b2;hpb=8dbb48ad299320b71e3d59eb79a8634f97aff6bb;p=jalview.git diff --git a/help/html/features/structurechooser.html b/help/html/features/structurechooser.html index b276897..fc71826 100644 --- a/help/html/features/structurechooser.html +++ b/help/html/features/structurechooser.html @@ -24,40 +24,111 @@
-- Structure Chooser -
++ Structure Chooser +
- The Structure Chooser panel was added in Jalview 2.8.3. It - introduced a smarter technique for selecting PDB structures to view in - Jalview by quering readily available meta-data of the structures. Some of the main features it provides are listed below: -+ The Structure Chooser interface allows you to interactively select + which PDB structures to view for the currently selected set of + sequences. It is opened by selecting the "3D + Structure Data.." option from the Sequence ID panel's pop-up menu. The dialog + provides: +
++ Selecting and Viewing Structures +
++ Once one or more structures have been selected, pressing the View + button will import them into a new or existing + structure view. +
++ Automated discovery of structure data +
+
+ 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.
+
+
+ Viewing existing + structures for your sequences +
++ If you have already loaded 3D structure data for the selected + sequences, the structure chooser will first open with the Cached + Structures View. 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. +
++ Selection of the best structure for each sequence +
+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).
+-
-
-
-
- Auto-Selection of Structures
-
+
The screenshot above shows the Structure Chooser interface
+ along with the meta-data of auto-discovered structures for the
+ sample alignment. If no structures were
+ auto-discovered, options for manually associating PDB records will be shown (see below).
+
+ Exploration of meta-data for available structures +
+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.
+
+
+
+ Manual selection/association of PDB files with
+ Sequences
+
To manually associate PDB files with a sequence, select 'From + File', or 'Enter PDB Id' from the drop-down menu: +
+ The Structure Chooser interface was introduced in Jalview + 2.9. +