[phenixbb] R, Rfree, and wxu_scale

[Jianghai Zhu]

I have tested different values for wxc_scale, seems like 0.05 gave me  
the best Rfree and smallest Rfree-R gap, which of course gave an  
excellent geometry statistics.  My starting model has ANISO in it and  
I always using individual sites+individual ADP+tls.  But then I can't  
test wxu_scale anymore since phenix.refine will just reset the  
wxu_scale.  Since the best way is to use tls every time, how do test  
wxu_scale?

Jianghai

+++++++++++++++++++++++++++++++
Jianghai Zhu, Ph.D
CBR Institute for Biomedical Research
Department of Pathology
Harvard Medical School
200 Longwood Ave., Boston, MA 02115
Ph: 617-278-3211
Fx: 618-278-3232
+++++++++++++++++++++++++++++++



On Aug 4, 2007, at 10:33 PM, Pavel Afonine wrote:

> Hi Jianghai,
>
>> Just finished a round of refinement.  Rfree went up about 1% and R
>> went down a bit.  I am wondering what happened here.
>
> You may want to play with wxc_scale and wxu_scale, that define  
> relative
> contribution of X-ray term in coordinate and ADP refinement,
> correspondingly. The corresponding weights, wxc and wxu, are  
> determined
> automatically and are good for most of the cases, but as always, there
> are some deviations (rarely significant).
>
> Try different values for wxc_scale: just an array of values differing
> from default by say 0.25, 0.5, 1.5, 2 times and choose the one that
> gives you the best Rfree, gap Rfree-Rwork and geometry statistics.  
> Same
> for wxu_scale. This always almost helps to resolve this kinds of  
> issues.
>
>> Also Rfree always went down after TLS refinement but always went up a
>> lot more after the individual ADP refinement.  Is there anything I  
>> can
>> do here?
>
> Here you must be careful. There are two potential traps to be aware of
> (these are not bugs but features that people have to be aware of):
>
> 1) If you do TLS first, the atoms in output file have ANISOU  
> records. If
> you then take that  output file and refine individual ADP (without  
> using
> TLS), by default they will be refined as anisotropic (since input file
> has ANISOU records and those atoms are considered as anisotropic).  
> This
> is most likely not what you want and also in this case Rfree may go up
> drastically.
> 2) If you force them to be refined isotropically, then the anisotropic
> atoms got converted to isotropic and hence both R and Rfree will go  
> up.
> This is also you may not want to do.
>
> So, the best, if you used TLS refinement once, keep using it in next
> refinements, otherwise you will fall into one of two traps above.
>
>> Should I use weaker B restraints?  I tried to assign a wxu_scale
>> value.  But phenix.refine automatically adjust it to 1.81 every time.
>
> This is intentional and always happens for TLS+ADP individual
> refinement. We found this the best by re-refining 350 models from PDB.
>
> All these questions are explained in depth in phenix.refine
> documentation in the next upcoming PHENIX release.
>
> Pavel.
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