[phenixbb] R, Rfree, and wxu_scale

Jianghai Zhu jzhu at cbr.med.harvard.edu
Sat Aug 4 19:50:55 PDT 2007

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  


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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20070804/33bdfb5f/attachment-0003.htm>

More information about the phenixbb mailing list