X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Ffeatures%2Fviewingpdbs.html;h=f60da1af5b69682a55b3003d93c94af9e37e106a;hb=54dd5d7c3c4384ef383ead7cf3d150ac5fddb3da;hp=353ca09aac7d5ad2473333b4e23c43edb5817740;hpb=83b541e967d19e6aeb5b02f476a77399f5f79d22;p=jalview.git diff --git a/help/html/features/viewingpdbs.html b/help/html/features/viewingpdbs.html index 353ca09..f60da1a 100755 --- a/help/html/features/viewingpdbs.html +++ b/help/html/features/viewingpdbs.html @@ -1,41 +1,203 @@ - -
Viewing PDB Structures
-Jalview has a simple 3D structure viewer which - can visualize polypeptide backbone structures associated with a sequence in - a particular alignment view. It is accessed via the "Sequence→View - PDB entry:" entry from the sequence's pop-up menu.
-Since Jalview 2.3, Jmol has been integrated into the application and will also - run in the applet in all latest web browsers. For more help using Jmol, see - http://jmol.sourceforge.net/docs/JmolUserGuide/ -
-To associate PDB files with a sequence, right click on a sequence ID and select - "Associate Structure with Sequence", and one of the submenus:
-Note: You can retrieve sequences from the PDB using the 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).
-Sequences which have PDB File associations are annotated with sequence features - from the group 'PDBFile' giving the corresponding PDB Residue Number for each - mapped residue in the seuqence. The display of these features is controlled through - the "View→Sequence Features" menu item and the - Feature Settings dialog box.
-See the PDB Viewer help page for more information.
- - + + + ++ Discovering and Viewing PDB Structures +
+ Jalview can be used to explore the 3D structures of sequences in an + alignment by following the steps below: +
+ Structure Viewers in the Jalview Desktop
+ 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. +
+
+ After pressing the
+ 'View' button in the Structure Chooser
The behaviour of
+ the 'View' button depends on the number of structures selected, and
+ whether structure views already exist for the selected structures or
+ aligned sequences.
+
+ If multiple structures are selected, then Jalview will always create
+ a new structure view. The selected structures will be imported into
+ this view, and superposed with the matched positions from the
+ aligned sequences.
If a single PDB structure
+ is selected, one of the following will happen:
+
+ Retrieving sequences from the PDB
You can
+ retrieve sequences from the PDB using the Sequence Fetcher. The sequences
+ retrieved with this service are derived directly from the PDB 3D
+ structure data, which can be viewed in the same way above. Secondary
+ structure and temperature factor annotation can also be added.
+
+
Jalview will also read PDB files directly - either in PDB
+ format, or mmCIF. Simply load in the file
+ as 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.
+
+ 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 by the
+ 'From File' entry of the structure menu.
+
+
+ Viewing the PDB Residue Numbering
+ Sequences which have PDB entry or PDB file associations are
+ annotated with sequence features from a group named with the
+ associated PDB accession number or file name. Each feature gives the
+ corresponding PDB Residue Number for each mapped residue in the
+ sequence. The display of these features is controlled through the "View→Sequence
+ Features" menu item and the Feature
+ Settings dialog box.
+
+ Switching between mmCIF and PDB format for
+ downloading files from the PDB
Jalview now employs the mmCIF format for importing 3D structure data
+ from flat file and EMBL-PDBe web-service, as recommended by the
+ wwwPDB. If you prefer (for any reason) to download data as PDB files
+ instead, then first close Jalview, and add the following line to
+ your .jalview_properties file:
+ PDB_DOWNLOAD_FORMAT=PDB
+
When this setting is configured, Jalview will only request
+ PDB format files from EMBL-EBI's PDBe.
mmCIF format
+ file support was added in Jalview 2.10.
+
+ Outstanding problem with cut'n'pasted
+ 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/browse/JAL-623 for news on this problem.
+