[phenixbb] Low resolution refinement

Randy John Read rjr27 at cam.ac.uk
Wed Nov 17 03:51:13 PST 2021

Also, these days I would recommend using an AlphaFold2 model as a reference model, unless you have the structure of a very closely-related homologue.


> On 16 Nov 2021, at 20:58, Pavel Afonine <pafonine at lbl.gov> wrote:
> Hi Armando,
>> 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 density;
> - 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!
> Good luck!
> Pavel
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Randy J. Read
Department of Haematology, University of Cambridge
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