Calculating structural properties and plotting them
===================================================

1. Run the :doc:`polyphony_plot_property` python script. This the -p property option lets you choose which property to plot e.g. 

.. code-block:: sh
    
   polyphony_plot_property.py -f clust_1PW6_A_95.fasta -p bfactor

The choices are defined in the \[properties] section of your :doc:`config` file. Until you install 3rd party software, these choices are quite limited. See :doc:`plugins` for how to add functionality. Here is a picture of what got when I did this.

.. image:: images/bfactors.png
    :scale: 50 %
    :align: center
    
You can zoom into parts of Matplotlib/pylab plots. Here is a screen capture after zooming onto the C-terminus.

.. image:: images/bfactors-zoomed.png
    :scale: 50 %
    :align: center


2. The first time you run a script the properties are calculated or read from the pdb files. These properties are then stored on disk so they don't need to be recalculated everytime an analysis is carried out. Use the *-u* option to use recalculated values from scratch for :doc:`polyphony_plot_property` and other scripts.

Before going further it might be an idea to do the following:

3. Run :doc:`polyphony_calculate_all_properties` in the directory containing your fasta file. e.g.
     
.. code-block:: sh
    
   polyphony_calculate_all_properties.py -f clust_1PW6_A_95.fasta
   
This will allow more interactive analysis in pymol and with scripts. If you have many residues in your alignment, go away and have a cup of tea (or go down the pub for really big files). When you come back all the property calculations should have finished, intermediate results stored and various output files produced in the current working directory.