X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fstructurechooser.html;h=296a751d12b6445440ecc03ceb8710b7d67aeeee;hb=53e232c25d1956fdcc239b0db8d6b18cecc601a4;hp=b276897cbdeb549585ede93ac809a683457ac6b2;hpb=8dbb48ad299320b71e3d59eb79a8634f97aff6bb;p=jalview.git
diff --git a/help/html/features/structurechooser.html b/help/html/features/structurechooser.html
index b276897..296a751 100644
--- a/help/html/features/structurechooser.html
+++ b/help/html/features/structurechooser.html
@@ -24,40 +24,104 @@
-
- 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
-
-
- 
-
-
-
- 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 any of
+ the follwing options listed below from the drop-down menu in the
+ interface:
+
+ - From File - You can 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 - Jalview will use the PDB
+ Rest API, provided by the EBI, to fetch the PDB file with the
+ entered Id.
+ - Cached PDB Entries - You can view PDB
+ structures which have previously been downloaded/viewed using this
+ option. Jalview caches previously downloaded PDB entries in the
+ computer memory. However, if the project is saved before exiting
+ Jalview, Jalview will serialize the cached entries to the file
+ system.
+
+
+
+ The Structure Chooser interface was introduced in Jalview
+ 2.9.
+