PDB Viewing

From: jprocter Date: Fri, 9 Dec 2005 18:48:09 +0000 (+0000) Subject: added description of how PDB structures can be associated with X-Git-Tag: Release_2_07~13 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=703dc2f29ede06dd51bef1940bb49f234cf35a0d;p=jalview.git added description of how PDB structures can be associated with sequences (and so viewed in the PDB viewer). --- diff --git a/help/html/features/viewingpdbs.html b/help/html/features/viewingpdbs.html new file mode 100755 index 0000000..1c50d2f --- /dev/null +++ b/help/html/features/viewingpdbs.html @@ -0,0 +1,29 @@ + +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 pop-up menu.

There are two ways to associate PDB files with sequences:

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).

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

+ +