PDB Viewing

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fviewingpdbs.html;h=506beef6e1f5df2316f89952f9d69e94c8abc46b;hb=c248aad32a357e7440b2e5ab3ea8c5fddbb26b84;hp=ad785492e21cb7baaa815475a31087d0d7ee19da;hpb=0696cffbccbb537be78d9fc2410589adbcd7be35;p=jalview.git diff --git a/help/html/features/viewingpdbs.html b/help/html/features/viewingpdbs.html index ad78549..506beef 100755 --- a/help/html/features/viewingpdbs.html +++ b/help/html/features/viewingpdbs.html @@ -1,70 +1,107 @@ + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + --> 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
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)

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.
See the Jmol - PDB viewer help page for more information about the display.

Chimera

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 WSDBFetch, provided by the - EBI, to discover PDB ids for all the sequences in the alignment which - have valid Uniprot names / accession ids.

Importing PDB Entries or files in PDB format
You can retrieve sequences from the PDB using the Sequence Fetcher. Any sequences retrieved with @@ -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.
+report at http://issues.jalview.org/browse/JAL-623 for news on this problem.