PCA trajectory alignment

[georgkempf]

Hello,

in the PCA tutorial there is an initial trajectory alignment step

aligner = align.AlignTraj(u, u, select='backbone',
                          in_memory=True).run()

which should align the trajectory to the first frame.

But then in the PCA instance

pc = pca.PCA(u, select='backbone',
             align=True, mean=None,
             n_components=None).run()

the alignment option is also activated. Based on the API docs this will also do an alignment of the trajectory to a reference structure.

My question is if the two alignment steps are redundant and if the align option in the PCA instance can be disabled when AlignTraj has been performed?

[orbeckst]

I think you're right (looking at the code and playing around briefly). But don't take my word, check yourself:

Did you try

1. AlignTraj, align=True
2. AlignTraj, align=False
3. align=True
4. align=False

and compared the results, e.g., the pc.variance or pc.cumulated_variance?

I'd think that (1), (2), and (3) all give pretty much the same answer.

Once you conclude that you're right, could you please open an issue in the User Guide https://github.com/MDAnalysis/UserGuide/issues to suggest a correction?