.. _alignment:

Alignment
---------

**Align coordinates**

pyanca offers two rigid-body alignment algorithms:

* Iterative alignment 

* Standard Kabsch alignment


.. Note:: **This step is not needed if we use dihedral/angular coordinates for the workflow.**
         
          *We assume that you have taken care of putting protein chains or independent molecules together
          in the trajectories before aligning them. Depending on which software you used for your simulations
          the procedures for putting together individual chains or molecules can be different.*