On Sun, Aug 24, 2014 at 9:34 PM, Pavel Afonine <pafonine@lbl.gov> wrote:
why not? You can arbitrarily choose one model and map as a reference and overlay the rest over it. Phenix tools such as "Structure comparison" or lower level ones such as phenix.superpose_maps and phenix.superpose_pdbs should help here. Nat spent time on this so I hope he offers more advice on this once he sees this email.

There isn't much to add to this, other than a more thorough description of what the programs do, which as usual, is not (yet) mentioned in our documentation:

- phenix.superpose_maps: given two models and two MTZ files containing map coefficients, superposes the models (using user-provided selections if desired), moves them into a P1 box (where all sites > [0,0,0]), then transforms the selected maps to follow.  Only works on one pair of map coefficients at a time, but allows any type of complex array to be used.

- structure comparison: given M models containing N copies of chain X, and M corresponding MTZ files, extracts all copies of chain X, superposes in a P1 box, transforms the maps to follow.  Works with any arbitrary number of models or chains, but limited to the most common map types (2mFo-DFc, mFo-DFc, anomalous).

We can make these methods more flexible if necessary - this is probably another set of code that's overdue for refactoring and consolidation anyway.

-Nat