[phenixbb] refinement

Pavel Afonine pafonine at lbl.gov
Thu Apr 2 08:11:06 PDT 2015

Hi Almudena,

even if you enable water update (add/remove/refine) phenix.refine will 
only do it if data resolution is higher than 2.8A. In case your data 
resolution is lower than 2.8A and you still want phenix.refine update 
water you need to set ordered_solvent.low_resolution to some large value 
like 3 or so.

In the GUI, ordered_solvent.low_resolution can be set as:

Refinement settings -> All parameters -> Ordered solvent -> Minimum 

If it still does not add water than perhaps data or current model 
quality isn't sufficient to do so automatically.


On 4/2/15 2:05 AM, Almudena Ponce Salvatierra wrote:
> Dear all,
> I am using Phenix.refine after MR and I have a complete model and data 
> to 2.8 Angstrom resolution. However, for some reason, Phenix does not 
> place any water molecules. Is there a setting I could change in order 
> to see whether this situation changes? What could the reason be?
> Thanks a lot in advance.
> Best,
> Almudena
> -- 
> Almudena Ponce-Salvatierra
> Macromolecular crystallography and Nucleic acid chemistry
> Max Planck Institute for Biophysical Chemistry
> Am Fassberg 11 37077 Göttingen
> Germany
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