X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fstructurechooser.html;h=d9582ec72f042f415283ee7d6c2da0b05e636165;hp=902bcdb248b83a57c4f004ffff4e4d204898a478;hb=db93a1adcbe0a4eaaf06e0a70ade0d6c5c1961c3;hpb=a90e2fe3cc3b779521a81cf8de410936f3a777c1 diff --git a/help/html/features/structurechooser.html b/help/html/features/structurechooser.html index 902bcdb..d9582ec 100644 --- a/help/html/features/structurechooser.html +++ b/help/html/features/structurechooser.html @@ -28,57 +28,51 @@ Structure Chooser
- 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 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: +
+ 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.
++ 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.
++ Selection of the best structure for each sequence +
+Jalview can automatically select the best structures according + to meta-data provided by the PDB. By default, the 'Best Quality' + structure for each sequence will 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).
@@ -94,30 +88,30 @@ be invoked as seen in the screenshot below.
+ style="width: 464px; height: 369px;">
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:
+ 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