[phenixbb] low-res. real-space refinement

Pavel Afonine pafonine at lbl.gov
Tue Mar 26 08:17:20 PDT 2013


Hi Oliver,

phenix.refine tries real-space refinement and if it increases R-factors 
above a certain threshold it rejects the result. You can't change this 
behavior it at present.
This will change once a new real-space refinement is in place (which 
will work well at any resolution, including very low).

Pavel

On 3/26/13 2:00 AM, "Weiergräber, Oliver H." wrote:
> Hello,
>
> when refining a protein structure against a low-resolution dataset (5 A), I wanted to also attempt real-space refinement.
> However, in the log file I find:
>
> |-real space refinement (target=simple)---------------------------------------|
>   rejected...
> |                                                                             |
> | --------------------------------------------------------------------------- |
>
> Changing the target to, e.g., diff_map does not change anything; the message will still refer to the "simple" target.
> I guess this is due to an internal resolution limit, but that's only speculation since it seems to be undocumented.
> Indeed, there is probably not much to be gained by real-space refinement at this resolution (at least not in terms of side-chain conformations), but I wanted to give it a try anyway.
>
> Any comments on this issue?
>
> Regards,
> Oliver
>
>
>
> ================================================
>    PD Dr. Oliver H. Weiergräber
>    Institute of Complex Systems
>    ICS-6: Structural Biochemistry
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