X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Ffeatures%2Fviewingpdbs.html;h=947b96b762b187cdaf8c167354aee2c6977b96a6;hp=b1ad4bae86c77cc534a3285c370a2a3e864cb54e;hb=e685afadb350fda906f1e360dfa30ad2cb476a2a;hpb=fb76e1a038151146946b6de40642eb415583cc1a
diff --git a/help/help/html/features/viewingpdbs.html b/help/help/html/features/viewingpdbs.html
index b1ad4ba..947b96b 100755
--- a/help/help/html/features/viewingpdbs.html
+++ b/help/help/html/features/viewingpdbs.html
@@ -24,7 +24,7 @@
- Discovering and Viewing PDB Structures
+ Discovering and Viewing PDB and 3D-Beacons structures
Jalview can be used to explore the 3D structures of sequences in an
alignment by following the steps below:
@@ -34,7 +34,7 @@
menu to open the Structure
Chooser dialog box.
- - If one or more structures exists for the given
+
- If one or more structures exist in the PDB for the given
sequence, the Structure
Chooser dialog will open with them listed in the results
pane.
@@ -43,9 +43,17 @@
href="structurechooser.html">Structure Chooser interface
will present options for manual association of PDB structures.
+ -
+ Since Jalview 2.11.2 you can also search the 3D-Beacons Network
+ for structures. The 3D-Beacons Network acts as a one-stop shop for protein
+ structures by combining and standardising data from several providers.
+ See 3D-Beacons Search for
+ instructions.
+
- Selecting Structures
You can select
+ Selecting PDB Structures
+ If one or more structures have been found from the PDB, you can select
the structures that you want to open and view by selecting them
with the mouse and keyboard.
By default, if structures were
discovered, then some will already be selected according to the
@@ -79,7 +87,8 @@
Structure Viewers in the Jalview Desktop
The
Jmol viewer has been included since Jalview
2.3. Jalview 2.8.2 included support for Chimera,
- provided it is installed and can be launched by Jalview. The default
+ provided it is installed and can be launched by Jalview. ChimeraX and PyMOL
+ support is included from Jalview 2.11.2. The default
viewer can be configured in the Structure
tab in the Tools→Preferences dialog box.
@@ -90,12 +99,14 @@
for more information.
- 
Controlling where the new structures
will be shown
+
+
The Structure Chooser offers several options
- for viewing a structure.
New View will open a new
+ for viewing a structure.
+ The Open new structure view button will open a new
structure viewer for the selected structures, but if there are views
already open, you can select which one to use, and press the Add
button. Jalview can automatically superimpose new structures based