Re: [phenixbb] Low resolution refinement

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. Randy

On 16 Nov 2021, at 20:58, Pavel Afonine 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 Cambridge Institute for Medical Research Tel: +44 1223 336500 The Keith Peters Building Fax: +44 1223 336827 Hills Road E-mail: [email protected] Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk