Yes, my stupid mistake. Please delete/disregard!
On 07/02/2015 12:46 PM, Robbie Joosten wrote:
But it is not the R-free of the shell here. In paired refinement you take the
R-free of the reflections outside the shell.
Cheers,
Robbie
Sent with my Windows Phone
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Van: Edward A. Berry <mailto:[email protected]>
Verzonden: 2-7-2015 18:43
Aan: [email protected] <mailto:[email protected]>
Onderwerp: Re: [ccp4bb] paired refinement
Another criterion for cutoff, also requiring the structure to be solved,
is the agreement between data and structure, e.g. Rfree or CCfree.
I think it is very unlikely that you could get Rfree =.2493 in a shell
which contains only noise. So I would suggest doing paired refinement
to 2.2 and 2.1 A (if the data is available).
On 07/01/2015 07:15 PM, Eric Karg wrote:
> Hi all,
>
> I have a dataset processed in XDS to 2.3 A (based on CC1/2). I'm trying to do
"paired refinement" to determine the optimal resolution cutoff. Here is what I get
at different resolutions set in Phenix:
>
> Final Rfree/Rwork:
> 2.7—> 0.2498/0.2027
> 2.6—> 0.2519/0.2009
> 2.5—> 0.2567/0.2025
> 2.4 —> 0.2481/0.2042
> 2.3 —> 0.2493/0.2075
>
> The geometry of all output structures are similar.
>
> 1. What is the high resolution cutoff based on these data? I know that
Rfree/Rwork at different resolution should not be compared, but is there a simple way
to do the test as described in the K&D 2012 Science paper using Phenix GUI?
>
> 2. For refining a structure at a lower resolution (lower than the initial
dataset), do I simply set the resolution limit in the refinement or I need to
reprocess the data starting from the images? Do I need to do anything with Rfree
flags? Based on the discussions on this forum I know I should deposit the highest
resolution dataset but my question is about the mtz file which will be used for
refinement.
>
> Thank you very much for your help!
>
