X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fviewingpdbs.html;h=44a07cc5847c567be8bf7a821c61d05584e63a6d;hb=023d23abaad346f745b93fced2407d7342ab7171;hp=2890b5dbe6c2e8347b18c915a0e6daa2d1473cf0;hpb=591878866313a3b0d5fa08b5c451255111ee2e92;p=jalview.git
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@@ -1,29 +1,149 @@
-
-PDB Viewing
-
-Viewing PDB Structures
-Jalview has a simple 3D structure viewer which can visualize polypeptide backbone
- structures associated with a sequence in an alignment. It is
- accessed via the "Sequence→View PDB
- entry:" entry from the sequence's pop-up menu.
-There are two ways to associate PDB files with sequences:
-
- - Select "Sequence Features" from
- the "View" menu, which retrieves any uniprot sequence
- records associated with the sequences in the alignment. If, for a
- particular sequence's uniprot record there
- are any cross-references to PDB structures, then these will be
- added to its list of associated database ids.
- - 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).
-
-For help on viewing and colouring structures see the PDB Viewer help page.
-
-
-
+
+
+
+PDB Viewing
+
+
+
+ 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
+ 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.
+
+
+
+If a single pdb
+structure is selected, one of the following will happen:
+
+
+ - If no structures are open, then an interactive display of the
+ structure will be opened in a new window.
+
+ - If another structure is already shown for the current
+ alignment, then you will be asked if you want to add and align this structure to the structure in
+ the existing view. (new feature in Jalview 2.6).
+
+ - If the structure is already shown, then you will be prompted
+ to associate the sequence with an existing view of the selected
+ structure. This is useful when working with multi-domain or multi-chain PDB files.
+
+ - See the Jmol
+ and Chimera PDB viewer help pages for more information about the display.
+
+
+
+Importing PDB Entries or files in PDB format
+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).
+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
+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.
+
+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.
+
+
+