[phenixbb] Restraints on water molecules

Pavel Afonine PAfonine at lbl.gov
Sun Mar 8 18:42:16 PDT 2009

Hi Engin,

Sorry for the inconvenience...

Water molecules are treated slightly different in phenix.refine than the 
other atoms. For example, you cannot preserve a specific water molecule: 
it it falls outside a selection criterion (distances, peak heights, 
etc...), than it will be removed anyway.

The only way to preserve your favorite waters is:

- either turn water picking off: ordered_solvent=false
- or do what you did: rename it somehow so phenix.refine "don't think" 
that it is water.

None of the above options sound attractive to me but this is how it is 
right now.

There are pros and cons for this approach and there was a discussion 
about it a few months ago. In the end I agreed that we need an option to 
preserve "user's favorite" waters.  It is in my list, implementing it 
may take some time - it's not very straightforward. In general, the 
whole water picking procedure in phenix.refine needs some review (for 
example, use map CC as additional criterion, etc...). Although I still 
don't like the idea for fixing waters: what if the user fixes a water 
that later on in refinement proves to be noise peak and so its B-factor 
jumps sky high, it moves somewhere, etc, but phenix.refine will not be 
able to remove it since the user ordered to not do so... Could you 
rather play with selection criteria so your waters stay?


On 3/8/09 4:02 PM, Engin Ozkan wrote:
> Are restraints on water molecules overwritten on successive cycles of 
> refinement where ordered solvent is on?  I seem to lose my distance 
> restraints between specific waters and metal, unless I name my water 
> molecules something else (and supply phenix with a cif for that name 
> which is identical to water inside). The distance restraints also seem 
> to be in effect for all cycles if ordered_solvent is off.
> I am also trying to make sure water numbers don't change during solvent 
> picking/deleting.
> Engin
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