X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fviewingpdbs.html;h=506beef6e1f5df2316f89952f9d69e94c8abc46b;hb=c248aad32a357e7440b2e5ab3ea8c5fddbb26b84;hp=6c10e98fa90c9c9907ba3c560a68a77e4db18ca4;hpb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;p=jalview.git
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PDB Viewing
-Viewing PDB Structures
+
+ 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.
+
+
-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:
- If no structures are open, then an interactive display of the
- structure will be opened in a new window
+ 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)
+ 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
- PDB viewer help page for more information about the display.
+ and Chimera PDB viewer help pages for more information about the display.
-
- 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:
-
-
- - From File - You can load a PDB file from the local machine or
- network and associate it with the selected sequence. PDB files
- associated in this way will also be saved in the Jalview Archive file.
-
-
- - Enter PDB Id - Jalview will use WSDBFetch, provided by the
- EBI, to fetch the PDB file with the entered Id.
-
- - 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
You can retrieve sequences from the PDB using the