PDB Viewing

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fviewingpdbs.html;h=75a5c9cd32bace353f9e504c84b7ecb72d0de62b;hb=71fc0e8716067e0d1100f82cced73c38bfb8d7f6;hp=9e549722ea9d332a0fb339805a8ef4acc1d888bd;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git diff --git a/help/html/features/viewingpdbs.html b/help/html/features/viewingpdbs.html index 9e54972..75a5c9c 100755 --- a/help/html/features/viewingpdbs.html +++ b/help/html/features/viewingpdbs.html @@ -1,68 +1,150 @@ -PDB Viewing + * 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

Jalview can view protein structures associated with a sequence via the "Structure→View - PDB entry:" entries from a sequence's pop-up menu. This will open an - interactive display of the structure in a new window, or prompt you - 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. +

+ 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
+

The "Structure→View + Structure→ submenu allows a single PDB structure to be chosen + for display from the available structures for a sequence. +
The "Structure→View all N + structures + option will open a new window containing all structures associated + with the current selection, superposed according to the currently selected region of the alignment.
This + capability was added in Jalview 2.7 +
The "Structure→View all N + representative structures + option will open a new window containing exactly one structure per + currently selected sequence.
+ The View representative structures option was introduced in + Jalview 2.8.1

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:

+ +

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.

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

+ href="seqfetch.html">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 seuqence. The -display of these features is controlled through the -"View→Sequence Features" menu item -and the Feature Settings dialog -box.
+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.
+