X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fviewingpdbs.html;h=6419525bb243963645a87cde9cf28d36ab2909fc;hb=141040cac1e8570634a25ad6a5550a56558041fb;hp=fc12b3bdbbd6b43c4fe346d1e707c418bab4798e;hpb=a45774ee31d9f35d4eff46d54d7deab719afb092;p=jalview.git
diff --git a/help/html/features/viewingpdbs.html b/help/html/features/viewingpdbs.html
index fc12b3b..6419525 100755
--- a/help/html/features/viewingpdbs.html
+++ b/help/html/features/viewingpdbs.html
@@ -1,87 +1,102 @@
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see
Viewing PDB Structures
++ Viewing PDB Structures +
+ Jalview can be used to view protein structures by following the steps below: ++ 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:
- Opening structures associated with the current selection
- If one or more of the sequences in the alignment are selected, then
- the Structure submenu of the Sequence
- ID popup menu will contain will include either a 'View all X
- structures' entry in the submenu or a 'View structure for Sequence'
- entry. Both these options will open a new Jmol view containing one, or
- 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:
- -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.
@@ -96,7 +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.