[phenixbb] Refining atoms on special positions

Pavel Afonine PAfonine at lbl.gov
Thu May 7 23:06:05 PDT 2009

Hi Oliver,

I'm not sure what's going on, since from what you described it seems 
like you doing what one should do.

If you send me the data and model I will be happy to have a look.

The fact the you get substantially lower R-factors in Refmac tells me 
that there must be an obvious fix in phenix.refine or in what you are 
trying to do using phenix.refine so it produces comparable or better 


On 5/7/09 12:36 AM, Oliver Clarke wrote:
> Hi,
> I'm running phenix.refine v1.4-3, and I'm refining a 3.3A structure  
> that has potassium ions present on a crystallographic fourfold axis. I  
> believe (based on previous refinement in REFMAC5.5), that these ions  
> are at full occupancy, so I set the occupancy of each ion to 1.
> Despite this, there is still a lot (several 7-10sigma peaks in the Fo- 
> Fc) of unexplained positive density, the potassium ions do not  
> converge to their previously refined positions, and their B-factors  
> refine upwards to values several times higher than the surrounding  
> protein. When the same structure is refined in refmac (with ion  
> occupancy set to 0.25), there is little to no unexplained density and  
> the R/Rfree are substantially lower (21.9/25.9 as against 24.5/31)
> Does anyone have any ideas/suggestions as to what might be going on?
> Cheers,
> Oliver
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