X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fviewingpdbs.html;h=e9f28d5f0067ad0f015e186173cd4ba4398a6bb8;hb=7c28880430765f06ccd5ec8ad3caf17871336e97;hp=2890b5dbe6c2e8347b18c915a0e6daa2d1473cf0;hpb=591878866313a3b0d5fa08b5c451255111ee2e92;p=jalview.git diff --git a/help/html/features/viewingpdbs.html b/help/html/features/viewingpdbs.html index 2890b5d..e9f28d5 100755 --- a/help/html/features/viewingpdbs.html +++ b/help/html/features/viewingpdbs.html @@ -1,29 +1,121 @@ - -
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:
-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. Once a pdb +structure is selected, one of the following will happen:
+ +
+ Opening structures associated with the current selection
+ If one or more of the sequences in the alignment are selected, then
+ the Structure submenu of the Sequence
+ ID popup menu will contain will include either a 'View all X
+ structures' entry in the submenu or a 'View structure for Sequence'
+ entry. Both these options will open a new Jmol view containing one, or
+ all the structures available for all selected sequences, superimposed
+ using the currently selected region of the alignment. (This
+ capability was added in Jalview 2.7)
+
Associating PDB files with Sequences
+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:
+ +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.
+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 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.