X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fviewingpdbs.html;h=99f17fe1c3388bd79d576d2b4fb6a5b721659bb6;hb=e8479b912a9f5caf2e86d2dee10f153955522e33;hp=a6f5de92aeb857e8cb762db906da14ad7f2b2f55;hpb=46e848e62edcdfd0a135d313128456bb69055009;p=jalview.git
diff --git a/help/html/features/viewingpdbs.html b/help/html/features/viewingpdbs.html
index a6f5de9..99f17fe 100755
--- a/help/html/features/viewingpdbs.html
+++ b/help/html/features/viewingpdbs.html
@@ -1,51 +1,89 @@
+ * 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
+
+ Jalview can view protein structures associated with a sequence via the
+ "Structure→" submenu from a sequence's pop-up menu.
+
+ 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.
+
+ The following menu entries are provided for viewing structure data
+
+ - The "Structure→View
+ Structure→ submenu allows a single PDB structure to be chosen
+ for display from the available structures for a sequence.
+
+ - The "Structure→View all N
+ structures
+ option will open a new window containing all structures associated
+ with the current selection, superposed according to the currently selected region of the alignment.
This
+ capability was added in Jalview 2.7
+
+ - The "Structure→View all N
+ representative structures
+ option will open a new window containing exactly one structure per
+ currently selected sequence.
+ The View representative structures option was introduced in
+ Jalview 2.8.1
+
+
-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
+
Associating PDB files with Sequences
+ 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:
@@ -60,9 +98,8 @@ Sequence", and one of the submenus:
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.
+ Discover PDB Ids - Jalview uses the sequence's ID to query WSDBFetch, provided by the
+ EBI, and any enabled DAS servers, to discover PDB ids associated with the sequence.
Importing PDB Entries or files in PDB format