X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fviewingpdbs.html;h=1f49498da88dbc013c856e6a395845fb4801ba6a;hb=e1cd94839128776e14e51ded3f3be2dcc7e72273;hp=679f35303af73c34f709b32761589352d37c64b0;hpb=793968f15efc19ba0b8a91b0078e6b23ee4e2ff9;p=jalview.git
diff --git a/help/html/features/viewingpdbs.html b/help/html/features/viewingpdbs.html
index 679f353..1f49498 100755
--- a/help/html/features/viewingpdbs.html
+++ b/help/html/features/viewingpdbs.html
@@ -1,21 +1,24 @@
+ * 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
@@ -23,8 +26,31 @@
Viewing PDB Structures
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
+via the "Structure→" submenu from a
+sequence's pop-up menu.
+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
+
+
+
+
+If a single pdb
structure is selected, one of the following will happen:
@@ -38,22 +64,12 @@ structure is selected, one of the following will happen:
- 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.
-
-
- Additionally, if several of the sequences in the currently selected
- region of the alignment have associated structures, then Jalview will
- provide a 'View X structures' entry in the submenu. This
- option will open a new Jmol view containing all the structures
- available for all selected sequences, superimposed using the currently
- selected region of the alignment. (This capability was added
- in Jalview 2.7)
-
-
+ 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:
@@ -69,9 +85,8 @@ 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