[phenixbb] secondary structure restraints helices/helixes proline
pafonine at lbl.gov
Wed May 2 23:16:33 PDT 2012
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
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.
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