X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Ffeatures%2Fstructurechooser.html;h=2c77049d23515dd5cf07a0134281aaa58dfef65e;hb=00a0552110d2d6a9f4e4da584b28d53fc3bfffd0;hp=11cad6b4b69fb63b6155178562c1f7655845bb3d;hpb=e685afadb350fda906f1e360dfa30ad2cb476a2a;p=jalview.git diff --git a/help/help/html/features/structurechooser.html b/help/help/html/features/structurechooser.html index 11cad6b..2c77049 100644 --- a/help/help/html/features/structurechooser.html +++ b/help/help/html/features/structurechooser.html @@ -67,13 +67,10 @@ Automated discovery of structure data
- After selecting "3D Structure Data ..", Jalview queries the PDB via
+ After selecting "3D Structure Data ..", Jalview queries its available structure data providers. When Uniprot identifiers are available, it queries the 3D-Beacons network (since Jalview 2.11.2), otherwise it searches 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.
-
- Since Jalview 2.11.2, you can also initiate a search
- of the 3D-Beacons Network.
Viewing existing @@ -91,16 +88,17 @@ 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 'PDBe 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
+ to meta-data provided by the search service. The 'PDBe Best Quality' structure for each sequence will
+ by default be selected when no other structure data is available. If 3D-models from other sources are also available, then 'Best 3D Beacons coverage' will be show.
+
Clicking on the drop down menu allows
+ other criteria to be chosen. For the PDBe, these include including Resolution (only defined for
+ X-Ray structures), Highest Protein Chain etc. When 3D-Beacons results are available, structures can be selected based on their specific provider, or by their coverage of the aligned sequences.
+
When 'Invert' is
selected, structures are selected in reverse order for the current
criteria (e.g. worst quality rather than best).
- +