[phenixbb] Low resolution refinement
xalbert at iqfr.csic.es
Wed Nov 17 04:54:24 PST 2021
Thank you all,
The MR solution comes from an alphaFold model. It packs well, it provides a sensible (biological) oligomer and a reasonable electron density (tubes for alpha helices). In any case, I am not sure about the solution. Phaser refinement seems to work and I wonder if I can progress with phenix.refine (or any other).
> El 17 nov 2021, a las 12:51, Randy John Read <rjr27 at cam.ac.uk> escribió:
> 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!
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> Randy J. Read
> Department of Haematology, University of Cambridge
> Cambridge Institute for Medical Research Tel: +44 1223 336500
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> Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
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