[phenixbb] overlapping electron density maps

Nathaniel Echols nechols at lbl.gov
Mon Aug 25 14:20:38 PDT 2014

On Sun, Aug 24, 2014 at 9:34 PM, Pavel Afonine <pafonine at 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

- 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.

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20140825/552e0080/attachment.htm>

More information about the phenixbb mailing list