X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Ffeatures%2Fviewingpdbs.html;h=b1ad4bae86c77cc534a3285c370a2a3e864cb54e;hb=978ff69a2fa5b918f8c39c10c0536f2872c8df27;hp=45d979f824e048a5046e49923797e220f182aedb;hpb=5bc4be3925cd553d5516c5eb10daf2e4259e475a;p=jalview.git diff --git a/help/html/features/viewingpdbs.html b/help/html/features/viewingpdbs.html index 45d979f..b1ad4ba 100755 --- a/help/html/features/viewingpdbs.html +++ b/help/html/features/viewingpdbs.html @@ -82,6 +82,7 @@ provided it is installed and can be launched by Jalview. The default viewer can be configured in the Structure tab in the Tools→Preferences dialog box. +
Structure data imported into Jalview can also be processed to display secondary structure and temperature factor annotation. See @@ -89,44 +90,30 @@ for more information.
- After pressing the
- 'View' button in the Structure Chooser
The behaviour of
- the 'View' button depends on the number of structures selected, and
- whether structure views already exist for the selected structures or
- aligned sequences.
+
Controlling where the new structures
+ will be shown
+
The Structure Chooser offers several options
+ for viewing a structure.
New View 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
+ on the linked alignments - but if this is not desirable, simple
+ un-tick the Superpose Structures checkbox.
+
If multiple structures are selected, then Jalview will always - create a new structure view. The selected structures will be - imported into this view, and superposed with the matched positions - from the aligned sequences. A message in the structure viewer's - status bar will be shown if not enough aligned columns were - available to perform a superposition.
- If a single PDB structure is selected, one of the
- following will happen:
+ Superposing structures
Jalview superposes structures using
+ the visible portions of any associated sequence alignments. A
+ message in the structure viewer's status bar will be shown if not
+ enough aligned columns were available to perform a superposition.
+ See the Jmol + and Chimera help pages for + more information about their capabilities.
+
Retrieving sequences from the PDB
You can