[phenixbb] phenix 1.3-rc4 vs. phenix 1.3-final

Paul Adams PDAdams at lbl.gov
Thu Sep 11 08:58:12 PDT 2008

Hi Jianghai,

   Pavel introduced an automatic modification of the weights between  
these two versions. In general it is an improvement but in some cases  
the final R-factors can be a bit higher than using fixed weights.  
Unfortunately there isn't a way to turn off this autoweighting in 1.3- 
final. Pavel will add this option and we'll release an updated  
installer soon (there are a couple of other bugs we've found  
elsewhere in PHENIX that are being fixed also).


On Sep 11, 2008, at 7:54 AM, Jianghai Zhu wrote:

> Hi,
> I have done a couple of refinements using either phenix.refine 1.3-rc4
> or phenix.refine 1.3-final.  And phenix.refine 1.3-rc4 always gave me
> a lower Rfree, about 1% lower than phenix.refine 1.3-final, which
> actually is pretty big.  What has changed between this two versions?
> -- Jianghai
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Paul Adams
Deputy Division Director, Physical Biosciences Division, Lawrence  
Berkeley Lab
Adjunct Professor, Department of Bioengineering, U.C. Berkeley
Vice President for Technology, the Joint BioEnergy Institute
Head, Berkeley Center for Structural Biology

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