[phenixbb] Restraints on water molecules

Engin Ozkan eozkan at stanford.edu
Sun Mar 8 21:52:54 PDT 2009

Thanks Pavel, you are as prompt and helpful as always.

I agree that fixing waters sounds like a very, very bad idea.  I am only 
thinking of adding restraints for waters coordinating metals (with 
appropriate sigma), where water-metal distance can easily get down to 2 
A (A possibly bigger issue that I haven't given much thought to might be 
that such a water ends up being very close  (~3.2-3.5 A) to four more 
metal-coordinating oxygens; that may look impossible from a hydrogen 
bonding water point-of-view).  Playing with water selection criteria 
would have global effects, quite significant in a structure with 800 
water molecules (as of yet). I think I'll stick with what I was doing, 
or maybe add a last ordered_solvent=False to the refinement at the end.


Pavel Afonine wrote:
> 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?
> Pavel.
> 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
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://www.phenix-online.org/mailman/listinfo/phenixbb
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb

More information about the phenixbb mailing list