X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fviewingpdbs.html;h=c342bc9d52e8177101c4782edc736f8ccf4a1d69;hb=f27f81a74bbe1be141d23df8aba578515e3179a2;hp=cf6671ec9091abf560a46e75d5793afbbb0e2c15;hpb=fd0e6b1ca56431d0aa68f64d8f5ff33bfee5b0ec;p=jalview.git
diff --git a/help/html/features/viewingpdbs.html b/help/html/features/viewingpdbs.html
index cf6671e..c342bc9 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
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
+
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:
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.Importing PDB Entries or files in PDB format
@@ -75,6 +112,18 @@ 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
extracted from the file and viewed in the alignment window.
+Associating a large number of PDB files to sequences
+in an alignment
It is often the case when working with
+structure alignments that you will have a directory of PDB files, and
+an alignment involving one or more of the structures. If you drag a
+number of PDB files onto an alignment in the Jalview desktop, Jalview
+will give you the option of associating PDB files with sequences that
+have the same filename. This means, for example, you can automatically
+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:
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
@@ -90,11 +139,11 @@ Features" menu item and the Feature
Settings dialog box.
Outstanding problem with cut'n'pasted
-files in Jalview 2.6
+files in Jalview 2.6 and Jalview 2.7
Structures imported via the cut'n'paste dialog box will not be correctly
highlighted or coloured when they are displayed in structure views,
especially if they contain more than one PDB structure. See the bug
-report at http://issues.jalview.org/JAL-623 for news on this problem.