Creating Jalview Feature files
==============================

Jalview is a very powerful sequence alignment viewer and editor. See :doc:`plugins` for more info. Here we will create a Jalview feature file for highlighting residues in the alignment and a dendrodram which can be used so sorting the sequences in an alignment.

.. code-block:: sh

    polyphony_write_jalview_feature_file.py -f clust_1PW6_A_95.fasta -p bfactor

Generates a file called *bfactor.ano*. This is a Jalview feature file which can be used to highlight residues with high temperature factors in a sequence alignment view.

.. code-block:: sh

    polyphony_write_newick.py -f clust_1PW6_A_95.fasta

Creates a file called *backbone.newick*. This is tree representation of the a clustering by backbone conformation. Use the -p option to specify alternative properties to use for the clustering.

Both these files can be read into Jalview like so:

1. Start Jalview
2. File > Input Alignment > from File  (read in your fasta file e.g. clust_1PW6_A_95.fasta)
3. A sequence alignment viewer window should open in that window
    1. File > Load Features/Annotations (read in bfactor.ano)
    2. File > Load Associated Tree (read in backbone.newick)
    3. Calculate > Sort > By Tree Order > /your_path/backbone.newick
    
You can now click on the tree view to colour sequences by cluster. You can also view the feature colours in 3D by e.g.

    4. right click on a structure label in the alignment view (e.g. 1PW6_B) > Structure > Associate Structure with Sequence > Enter PDB id > 1PW6
    5. right click on same structure label in the alignment view > Structure > View Structure > 1PW6

The results should look something like this (after a bit of fiddling with windows and fonts etc.)

.. image:: images/jalview.png
    :scale: 50 %
    :align: center