PDB Viewing

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Ffeatures%2Fviewingpdbs.html;h=353ca09aac7d5ad2473333b4e23c43edb5817740;hb=83b541e967d19e6aeb5b02f476a77399f5f79d22;hp=2890b5dbe6c2e8347b18c915a0e6daa2d1473cf0;hpb=591878866313a3b0d5fa08b5c451255111ee2e92;p=jalview.git diff --git a/help/html/features/viewingpdbs.html b/help/html/features/viewingpdbs.html index 2890b5d..353ca09 100755 --- a/help/html/features/viewingpdbs.html +++ b/help/html/features/viewingpdbs.html @@ -2,28 +2,40 @@ 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 Jalview has a simple 3D structure viewer which + can visualize polypeptide backbone structures associated with a sequence in + a particular alignment view. 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:

Since Jalview 2.3, Jmol has been integrated into the application and will also + run in the applet in all latest web browsers. For more help using Jmol, see + http://jmol.sourceforge.net/docs/JmolUserGuide/ +

To associate PDB files with a sequence, right click on a sequence ID and select + "Associate Structure with Sequence", and one of the submenus:

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).
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.

-For help on viewing and colouring structures see the PDB Viewer help page. -

Note: 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).

Sequences which have PDB File associations are annotated with sequence features + from the group 'PDBFile' giving 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.

See the PDB Viewer help page for more information.