X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fstructurechooser.html;h=785c42978170887d5250aaa472945b1b8c421cb5;hb=6f9d7b98943ecba292a9c0dd65b30c4d8150c98f;hp=f5f5916ed98d0517676a7e0b9807e1137fb982d4;hpb=d0771875f23ab994c4f85fb6cd604378768df10e;p=jalview.git diff --git a/help/html/features/structurechooser.html b/help/html/features/structurechooser.html index f5f5916..785c429 100644 --- a/help/html/features/structurechooser.html +++ b/help/html/features/structurechooser.html @@ -25,98 +25,109 @@
- Structure Chooser + Structure Chooser Dialog Box
- The Structure Chooser interface provides a smart technique for - selecting PDB structures to view in Jalview by querying readily - available meta-data of structures. The Interface can be invoked by - selecting the - "3D Structure Data.." option from a sequence's - pop-up menu. Some of the main - features it provides are listed below: ++ The Structure Chooser allows you to select + 3D 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 +
+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.
++ Once one or more structures have been selected, pressing the View + or Add button will import them a new or existing + structure view. When multiple views are available, use the + drop-down menu to pick the target viewer for the structures. +
++ 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).
-
+
-
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.
+
The screenshot above shows the Structure Chooser displayed after
+ selecting all the sequences in the Jalview example project. 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.
-
+ style="width: 464px; height: 173px;">
+
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: +
To manually associate PDB files with a sequence, select 'From + File', or 'Enter PDB Id' from the drop-down menu: