Hi Peter, general answer about how the whole thing works, see this: http://cci.lbl.gov/~afonine/rsr.pdf Specifically:
- How Phenix chooses which rotamers need to be fixed ?
see above.
- Does Phenix really re-calculate the three maps after correcting each rotamer ?
no, it happens only after one walk-through the all residues. In future this will be optimize to improve memory consumption.
-Can you please explain how fix_rotamers works together with ncs restraints ?
The whole procedure is not aware of NCS, or, actually, NCS should be smarter. This is in our plans to make better. Also, fix_rotamers may not perform as good as desired at lower resolutions. For this case we also have a number of things to work on, such as automatically using B-factor sharpened maps, locally-scaled maps, etc... Pavel.