PDB Viewing

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fviewingpdbs.html;h=d979254bc39181c5f97284ec772306b4b2a3e6a1;hb=c53aeee9a688f68d64106a968876e542f701fbc6;hp=ef222b135bf9b109e3bd5db37891df4e6a979cc6;hpb=2eeea2f43d7bbaafd79ebd4185b42fc60646d9e3;p=jalview.git diff --git a/help/html/features/viewingpdbs.html b/help/html/features/viewingpdbs.html index ef222b1..d979254 100755 --- a/help/html/features/viewingpdbs.html +++ b/help/html/features/viewingpdbs.html @@ -1,32 +1,68 @@ - -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.

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 - can 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).

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

- - + + +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:

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.

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.

+
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.
+ +