[phenixbb] Low resolution refinement

[Randy John Read]

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 <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
> 
> 
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
> Unsubscribe: phenixbb-leave at phenix-online.org

-----
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: rjr27 at cam.ac.uk
Cambridge CB2 0XY, U.K.                              www-structmed.cimr.cam.ac.uk