X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fviewingpdbs.html;h=506beef6e1f5df2316f89952f9d69e94c8abc46b;hb=43d326c3a7616aedecfce6f7980b3831ec25243a;hp=c342bc9d52e8177101c4782edc736f8ccf4a1d69;hpb=ad15cff29620f960119f80176f1fd443da9f6763;p=jalview.git
diff --git a/help/html/features/viewingpdbs.html b/help/html/features/viewingpdbs.html
index c342bc9..506beef 100755
--- a/help/html/features/viewingpdbs.html
+++ b/help/html/features/viewingpdbs.html
@@ -23,12 +23,29 @@
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.
+ Viewing PDB Structures
+ Jalview can be used to view protein structures by following the steps below:
+
+ - Select the "View Structure" option from a
+ sequence's pop-up menu to invoke the Structure Chooser interface.
+
+ - If one or more structures exists for the given sequence, the Structure Chooser
+ dialogue is opened with a list of the found structures meta-data.
+ - However, if no structure was found, the Structure Chooser interface is opened with options for manual association of PDB structures.
+
+
+ - Choose the structure to view from the discovered list. This can be done either manually by clicking directly
+ on the desired structure(s) in the list, or automatically by
+ using the drop-down menu on the interface to filter and auto-select the best structure based on certain
+ criteria like quality, resolution, etc.
+ - When the desired structure(s) have been selected, they can be
+ viewed by clicking the "View" button below the summary list.
+
+
+
+
The
Jmol viewer has been included since Jalview
2.3. Jalview 2.8.2 included support for Chimera, provided it is
@@ -42,7 +59,8 @@
href="xsspannotation.html">Annotation from Structure page for
more information.
- The following menu entries are provided for viewing structure data
+
-
If a single pdb
+
If a single pdb
structure is selected, one of the following will happen:
@@ -82,25 +100,7 @@ structure is selected, one of the following will happen:
- See the Jmol
and Chimera PDB viewer help pages for more information about the display.
- 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:
-
- - 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 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
You can retrieve sequences from the PDB using the