Question r/e PCA in MDAnalysis

[Dhanushka Weerakoon]

Hello,

I have a protein trajectory made up of multiple units in which all alpha carbons are pre-aligned to a crystal structure. I then want to run PCA on one unit. To decide whether to use the align argument in the pca.PCA class, I took a look into the source code and realised that on calculating the mean of the trajectory, the .run() method of the class appears to calculate the mean of the un-aligned trajectory? See the image, which part of the _prepare function - as I understand there should be an extra line within the if self.align statement:

self.mean += mobile_atoms.positions

If I have misunderstood I apologise - but if this is the case, would you suggest using my pre-aligned trajectory for PCA calculation and simply setting align=False?

Best wishes,

Dhanushka Weerakoon