[phenixbb] Gap between R and Rfree
Kendall Nettles
knettles at scripps.edu
Thu Feb 25 10:37:07 PST 2010
Did you check your data for anisotropy at the UCLA server? This solved
a similar problem for me
Kendall
On Feb 25, 2010, at 12:43 PM, "Young-Jin Cho" <yjcho at brandeis.edu>
wrote:
>
> Thanks for your suggestions, Phill.
> When I did Ramachandran analysis, it shows 96.60% in preferred
> region and 2.62% in allowed regions, and 0.79% is in outlier.
> Geometry looks Ok. I also did optimize_wxc and optimize_wxu, and tls
> option. it didn't help much.
> Now I am trying to scale down.
>
> Thanks again.
>
> Young-Jin
>
>
> 0. Use Molprobity or the Validation tools in Coot to look at your
> structure and see what errors you can fix.
> 1. What is your geometry like ? Try reducing wxc_scale (try
> wxc_scale=0.5) and see what happens.
> 2. What is the variation of B-factors across bonds ? Try reducing
> wxu_scale - perhaps wxu_scale=0.5 or less.
> 2a. phenix.refine is autocratic about wxu_scale if you're using TLS
> so
> setting it yourself does not help.
> 3. Since R-free of 0.298 is a little high for a 2.5 Angstrom
> structure,
> you should carefully check your model. Perhaps you have a high
> proportion of disordered structure, which can cause this. If you feel
> that your model is correct, you could explore using TLS on your model.
> Potential TLS groups can be found using the TLSMD server at:
> http://skuld.bmsc.washington.edu/~tlsmd/ although the results should
> always be filtered through a common-sense definition of domain/group
> boundaries (e.g. don't break in the middle of helices unless there's a
> good reason to).
>
> Phil Jeffrey
> Princeton
>
>
> Young-Jin Cho wrote:
>> Hi everyone,
>> I recently got a diffraction data and am trying to refine it. The
>> question is whatever I did the gap between R and Rfree stay far
>> away: .2140/.2982 around 2.5 A resolution. (water added and
>> isotropic(individual_adp) and so on).
>> Although I am redoing with many different approaches, if anyone can
>> give me any comments or suggestions, it would be helpful.
>>
>> Thanks in advance,
>>
>> Young-Jin
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
>
> --
> Postdoctoral Fellow, Kern Lab
> Biochemistry Department/HHMI
> Brandeis University
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
More information about the phenixbb
mailing list