[phenixbb] question about pick water in autobuild

Pavel Afonine PAfonine at lbl.gov
Sun Sep 6 22:45:37 PDT 2009


I hope Tom gives you the answer about how to stop water picking in 

 From my side, I'm wondering why it bothers you (I'm not saying that not 
working option is good)? Why don't you consider those waters as a tool 
for improving your map? You are free to remove any of them them later 
on. This can be viewed as a prototype of what ARP/wARP does, or other 
"density growing" techniques... In your case you just temporarily place 
waters where the model is still absent, and when you build those missing 
places just consider waters as density peaks (I hope model building 
programs assume waters as just density peaks and remove waters if they 
are on the macromolecule's way). On the other hand, model incompleteness 
may make the map ugly even for relatively well defined places.


On 9/6/09 7:38 AM, crystallogrphy wrote:
> Hi,
> I am building a model against a 2.1A data set using phenix.autobuild. 
> Right now Rfree is about 35%. I do not want to pick water in this 
> stage because I see denisty at N-terminal of my model which need to 
> build more residues. However, the program still picks water even after 
> I say 'place_waters=False'. Does anyone know why?
> phenix.autobuild data=exptl_fobs_phases_freeR_flags.mtz 
> model=AutoBuild_run_4_/overall_best-090905a.pdb seq_file=../ztb-sd.seq 
> refinement.place_waters=False refinement.refine_with_ncs=True nproc=2
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