X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fviewingpdbs.html;h=45d979f824e048a5046e49923797e220f182aedb;hb=bf97c293ad31f6ed5006a97d3a7d079c032652e8;hp=e62b2a78d9c274731156e6259f17473a57e3e165;hpb=ac4f3dfaa8d22b7b2eb164cceb354d029c07b0ad;p=jalview.git diff --git a/help/html/features/viewingpdbs.html b/help/html/features/viewingpdbs.html index e62b2a7..45d979f 100755 --- a/help/html/features/viewingpdbs.html +++ b/help/html/features/viewingpdbs.html @@ -46,38 +46,61 @@
+ 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
+ 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 the Annotation from Structure page 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.
+
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: @@ -89,8 +112,8 @@
- Retrieving sequences from the PDB
Jalview
- will also read PDB files directly - either in PDB format, or mmCIF. Simply load in the file as you would
- an alignment file. The sequences of any protein or nucleotide chains
- will be extracted from the file and viewed in the alignment window.
+
+
Jalview will also read PDB files directly - either in PDB
+ format, or mmCIF. Simply load in the file
+ as you would an alignment file. The sequences of any protein or
+ nucleotide chains will be extracted from the file and viewed in the
+ alignment window.
@@ -151,7 +173,7 @@ Features" menu item and the Feature Settings dialog box.
-
Switching between mmCIF and PDB format for
@@ -161,7 +183,7 @@
wwwPDB. If you prefer (for any reason) to download data as PDB files
instead, then first close Jalview, and add the following line to
your .jalview_properties file:
- DEFAULT_STRUCTURE_FORMAT=PDB
+ PDB_DOWNLOAD_FORMAT=PDB
When this setting is configured, Jalview will only request
PDB format files from EMBL-EBI's PDBe.
mmCIF format
file support was added in Jalview 2.10.