[phenixbb] Rigid body refinement question

Pavel Afonine PAfonine at lbl.gov
Thu Apr 29 20:43:39 PDT 2010

> During rigid-body refinement, the bonds/angles/dihedrals/nonbondeds
> to the non-refined sites are not restrained. This could seriously
> mess up the geometry.

Just to clarify: all the above parameters do not change for all atoms 
within the rigid group. They can get distorted at the border: say you 
split a chain into two rigid groups, then the bond corresponding to a 
hinge point where the one rigid group ends and the second one starts, 
can get distorted.

You can do torsion angle SA which is constrained rigid body refinement: 
the whole molecules is split into tiny rigid bodies and they are refined 
without breaking the stereochemistry.


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