X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Ffeatures%2Fviewingpdbs.html;h=6419525bb243963645a87cde9cf28d36ab2909fc;hb=141040cac1e8570634a25ad6a5550a56558041fb;hp=a6f5de92aeb857e8cb762db906da14ad7f2b2f55;hpb=46e848e62edcdfd0a135d313128456bb69055009;p=jalview.git
diff --git a/help/html/features/viewingpdbs.html b/help/html/features/viewingpdbs.html
index a6f5de9..6419525 100755
--- a/help/html/features/viewingpdbs.html
+++ b/help/html/features/viewingpdbs.html
@@ -1,78 +1,102 @@
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
PDB Viewing
-Viewing PDB Structures
+
+ Viewing PDB Structures
+
+ Jalview can be used to view protein structures by following the steps below:
+
+ - Select the "3D Structure Data..." option from a
+ sequence's pop-up menu to open the Structure Chooser dialog box.
+
+ - If one or more structures exists for the given sequence, the Structure Chooser
+ dialog will open with them listed in the results pane.
+ - However, if no structure was found, the Structure Chooser interface will present options for manual association of PDB structures.
+
+
+ - Selecting Structures
If structures
+ have been discovered, then some will already be selected according
+ to predefined selection criteria, such as structures with the
+ highest resolution. Use the drop down menu to select structures
+ according to different criteria, or, alternatively, choose
+ structures manually by selecting with the keyboard and mouse.
+
+ - Viewing Cached Structures
If you
+ have previously downloaded structures for your sequences, they
+ can be viewed by selecting the Cached PDB
+ Entries option from the drop down menu at the top of the
+ dialog box.
+
+ - To view selected structures, click the "View"
+ button.
+
+
+
+ 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.
+
-Jalview can view protein structures associated with a sequence
-via the "Structure→View PDB entry:" entries from a
-sequence's pop-up menu. Once a pdb
+
If a single PDB
structure is selected, one of the following will happen:
- If no structures are open, then an interactive display of the
- structure will be opened in a new window
+ structure will be opened in a new window.
- If another structure is already shown for the current
alignment, then you will be asked if you want to add and align this structure to the structure in
- the existing view. (new feature in Jalview 2.6)
+ the existing view. (new feature in Jalview 2.6).
- If the structure is already shown, then you will be prompted
to associate the sequence with an existing view of the selected
- structure.
+ structure. This is useful when working with multi-domain or multi-chain PDB files.
- See the Jmol
- PDB viewer help page for more information about the display.
+ and Chimera PDB viewer help pages for more information about the display.
-To associate PDB files with a sequence, right click on a sequence
-ID and select "Structure→ Associate Structure with
-Sequence", and one of the submenus:
-
-
- - From File - You can load a PDB file from the local machine or
- network and associate it with the selected sequence. PDB files
- associated in this way will also be saved in the Jalview Archive file.
-
-
- - Enter PDB Id - Jalview will use WSDBFetch, provided by the
- EBI, to fetch the PDB file with the entered Id.
-
-
- - Discover PDB Ids - Jalview uses WSDBFetch, provided by the
- EBI, to discover PDB ids for all the sequences in the alignment which
- have valid Uniprot names / accession ids.
-
-
Importing PDB Entries or files in PDB format
You can retrieve sequences from the PDB using the Sequence Fetcher. Any sequences retrieved with
+ href="pdbsequencefetcher.html">Sequence Fetcher. Any sequences retrieved with
this service are automatically associated with their source database
entry. For PDB sequences, simply select PDB as the database and enter
your known PDB id (appended with ':' and a chain code, if desired).
Jalview will also read PDB files directly. Simply load in the file as
-you would an alignment file. The sequences of any peptide chains will be
+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.
@@ -87,7 +111,7 @@ associate PDB files with names like '1gaq.pdb' with sequences that
have an ID like '1gaq'.
Note: This feature was added in Jalview 2.7
-Note for jalview applet users:
+Note for Jalview applet users:
Due to the applet security constraints, PDB Files can currently only be
imported by cut and paste of the PDB file text into the text box opened
by the 'From File' entry of the structure menu.