[phenixbb] secondary structure restraints helices/helixes proline

Pavel Afonine pafonine at lbl.gov
Wed May 2 23:16:33 PDT 2012

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.


> 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

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