Hi Morten, unless you turn on secondary structure restraints phenix.refine would not do anything special about secondary structure. If you use secondary structure restraints then I would check the automatically generated parameter file to see what phenix.refine "thinks" the secondary structure is, and also check the .geo file which is a footprint of all geometry restraints used in refinement reported for all atoms. Also, you can do simple geometry idealization (without using any diffraction data): phenix.pdbtools model.pdb --geom macro_cycles=100 to quickly see what is "ideal" according to the library that phenix.refine is using. Pavel

Hi guys,

How does phenix.refine handle prolines in helices? When I look in high resolution structures it seems that the carbonyl of the residue four positions before the proline (also in the helix) should be more perpendicular than parallel to the helix. This makes sense since there isn't any nitrogen for it to hydrogen bond to. But when I refine my structure it seems as if phenix.refine is trying to push the carbonyl into parallel position. Am I imagining things? It's not the best data and this is a troublesome region.

Cheers, Morten