X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fstructurechooser.html;h=daa1ac3cff20873daadc57bf0086030a4120bf0b;hb=9c66e390c2195d640a50bb645655c12158454f1e;hp=b276897cbdeb549585ede93ac809a683457ac6b2;hpb=8dbb48ad299320b71e3d59eb79a8634f97aff6bb;p=jalview.git
diff --git a/help/html/features/structurechooser.html b/help/html/features/structurechooser.html
index b276897..daa1ac3 100644
--- a/help/html/features/structurechooser.html
+++ b/help/html/features/structurechooser.html
@@ -24,40 +24,98 @@
-
- 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:
-
- - Automatic discovery, retrieval and association of PDB entries
- for an alignment's sequences
- - Visualisation of discovered structures' meta-data
- - Ability to configure the meta-data entries to visualise
- - Auto-selection of the best structure via filtering by
- the available metric parameters in the meta-data (i.e. resolution,
- quality etc).
- - Selection of multiple structures in a single operation
-
- Additionally, the Structure Chooser retains the following contemporary
- feature of Jalview:
-
- - Manual association of PDB entries via entering the PDB Id or
- From File
- - Ability to view cached PDB entries
-
+
+ The Structure Chooser interface allows you to interactively select
+ which PDB structures to view for the currently selected set of
+ sequences. It's opened by selecting the "3D
+ Structure Data.." option from the Sequence ID panel's pop-up menu. The dialog
+ provides:
+
+
+ - Automatic discovery, retrieval and association of PDB
+ entries for sequences
+ - Exploration of meta-data for available 3D structures
+ - Automatic selection of the 'best structure' to display for
+ each sequence
+ - Manual association of PDB entries by entering a PDB Id
+ - Association of structure data from a local file (in mmCIF
+ or PDB format)
+
- 
-
-
-
- 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. Note however that if no structures were
+ auto-discovered, a different interface for manual association will
+ be invoked as seen in the screenshot below.
+
+ 
+
+ 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:
+
+ - From File - 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 Jalview Archive file.
+ - Enter PDB Id - 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.
+
+
+ Viewing existing structures for your sequences
+
+
+ If you have previously associated structure data on the alignment,
+ selecting Cached PDB Entries from the drop down
+ menu allows you to select these structures for display.
+
+
+
+ The Structure Chooser interface was introduced in Jalview
+ 2.9.
+