X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fviewingpdbs.html;h=b1ad4bae86c77cc534a3285c370a2a3e864cb54e;hb=06beaa2f6eb56b94f4dd6408078a14e572cf0eb3;hp=e62b2a78d9c274731156e6259f17473a57e3e165;hpb=ac4f3dfaa8d22b7b2eb164cceb354d029c07b0ad;p=jalview.git diff --git a/help/html/features/viewingpdbs.html b/help/html/features/viewingpdbs.html index e62b2a7..b1ad4ba 100755 --- a/help/html/features/viewingpdbs.html +++ b/help/html/features/viewingpdbs.html @@ -46,64 +46,74 @@
+ 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.
+
+
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 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
@@ -112,13 +122,12 @@
retrieved with this service are derived directly from the PDB 3D
structure data, which can be viewed in the same way above. Secondary
structure and temperature factor annotation can also be added.
-
- 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 +160,7 @@ Features" menu item and the Feature Settings dialog box.
-
Switching between mmCIF and PDB format for
@@ -161,7 +170,7 @@
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.