X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fviewingpdbs.html;h=506beef6e1f5df2316f89952f9d69e94c8abc46b;hb=4f9d1e48b9d0231de697b36971311e4908490762;hp=9e549722ea9d332a0fb339805a8ef4acc1d888bd;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git diff --git a/help/html/features/viewingpdbs.html b/help/html/features/viewingpdbs.html index 9e54972..506beef 100755 --- a/help/html/features/viewingpdbs.html +++ b/help/html/features/viewingpdbs.html @@ -1,68 +1,149 @@ -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. -

-

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:

+

+ Viewing PDB Structures +

+ Jalview can be used to view protein structures by following the steps below: +
    +
  1. 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.
      • +
    +
    2. +
  2. 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.
    3. +
  3. When the desired structure(s) have been selected, they can be + viewed by clicking the "View" button below the summary list. +
    4. + +
+ + 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:

+ + +

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.

+