[phenixbb] Low resolution refinement
pafonine at lbl.gov
Tue Nov 16 12:58:00 PST 2021
> I have got a very promising MR solution at 5A resolution. Can I refine this structure? Any hint would be very much appreciated
this is a low resolution indeed, so modeling and refinement is likely to
be challenging. All the standard 'low-resolution refinement' advises
apply here. Since there are few data (low-res) you need to employ as
much 'a priori' known information as possible, in form of restraints
or/and constraints. Those typically include:
- If NCS is present, use NCS constraints (yes, constraints, not
restraints, as at this resolution you are highly unlikely to see
data-supported genuine differences between NCS copies!);
- if similar homologous models obtained at higher resolution are
available -- try using them as reference models;
- Use secondary structure restraints. Important: make sure to obtain
secondary structure annotation as accurately as possible.
- Use Ramachandran plot restraints (to avoid appearing outliers during
refinement, not to fix existing ones!);
- Avoid stretching your imagination by adding model in the absence of
- At this resolution refining group B factors (two B per residue) may be
a good idea.
Let me know if you have any more specific questions!
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