PDB Viewing

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fviewingpdbs.html;h=353ca09aac7d5ad2473333b4e23c43edb5817740;hb=83b541e967d19e6aeb5b02f476a77399f5f79d22;hp=6e47707a60d07a9c109b8f94966eea09ad83e1e4;hpb=c37851e9df086bcec69f32cf5067024e4dcdb01d;p=jalview.git diff --git a/help/html/features/viewingpdbs.html b/help/html/features/viewingpdbs.html index 6e47707..353ca09 100755 --- a/help/html/features/viewingpdbs.html +++ b/help/html/features/viewingpdbs.html @@ -1,37 +1,41 @@ - -PDB Viewing - -

Viewing PDB Structures

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.

To associate PDB files with a sequence, right click on a sequence ID and select - "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.

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.

- - + +PDB Viewing + +

Viewing PDB Structures

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.

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:

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.

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.

+ +