[phenixbb] Constrained occ refinement -- sum not equal 1

Pavel Afonine PAfonine at lbl.gov
Tue Feb 10 14:18:23 PST 2009

Hi Anne,

> Thanks for the quick reply. I downloaded the files, and I got the 
> result you predicted - all the occupancies looked neat and tidy as 
> expected. Since you used those nice occupancies to generate perfect 
> data, which was then refined against, that's what one would expect, 
> right? 

The occupancies in starting model, "start.pdb", are all garbage. So, if 
phenix.refine does something wrong with occupancy refinement, they would 
never refine to correct values.

> So I am still left with the issue of the occupancies going nuts in my 
> real refinement.

The test I did completely replicate the real situation: obviously, 
phenix.refine "does not know" that data.mtz contained fake Fobs -:)
If you are still getting the wrong values then there must be something 
else going not right. The only way to find out is if you send me the 
data and model and the exact command you used. In this case I will be 
able to reproduce the problem myself, investigate some more and 
hopefully provide a fix.

If you decide to send me the data, please make sure you send it to my 
address only and not to the whole bb.


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