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Ribbon diagram
================================

`Ribbon diagrams <https://en.wikipedia.org/wiki/Ribbon_diagram>`_ are 3D schematic representations of protein structure. The :mod:`Ribbon <batoms.ribbon.Ribbon>` object controls various settings related with ribbon diagram. Here are the secondary structures that supported:

    - α helix
    - β sheet
    - turn
    - HETATM (ligands, solvent ...)

Import a PDB file
==================

You can import a PDB data direct from the website `Protein Data Bank (RSCB) <http://www.rcsb.org/>`_ by:

.. code:: python

    from batoms.plugins.rscb import rscb_import
    protein = rscb_import("1ema")

Or you can read a local pdf file downloaded by yourself:

.. code:: python

    from batoms.pdbparser import read_pdb
    atoms = read_pdb("test/datas/1tim.pdb")
    protein = Batoms("1tim", from_ase = atoms)


Draw ribbon diagram
=====================

.. code:: python

    protein.ribbon.draw()

.. image:: /images/ribbon-1ema.png
   :width: 8cm

Selections
==================

You can select the secondary structures, and make change to them. For exmaple, show the atoms for a secondary structure by:

.. code:: python
    
    sel1 = protein.selects.add("sel1", "sheet A-160-A-170")
    sel1.show = True
    sel1.model_style = 1


.. image:: /images/ribbon-1ema-2.png
   :width: 8cm