[phenixbb] explicit solvent in low resolution refinement

Guenter Fritz guenter.fritz at uni-konstanz.de
Tue Nov 25 03:13:54 PST 2014

Hi Pavel,

yes, I see your point and I fully agree. My motivation is simple:
I hoped to get better phases from a model including water molecules, 
i.e. better maps for those parts of the model, which are still not very 
well defined. I feel at low resolution we fight for every tiny little 
bit of information that could improve the model. So I found it an 
attractive idea to use structured water. It is somewhat analogous to the 
concept to add restraints by the use of reference models derived from 
structures determined seperately , although these parts might look 
slightly different in the complex.

Finally to evaluate which water molecules might be there or not could be 
judged by running parallel refinement runs with several dozens of models 
including different water molecules. Good luck, this is not a big deal 

But  all in all, so far my trials in one specific case  yielded only a 
moderate improvement.

Best wishes, Guenter

> Hi Guenter,
> while I clearly understand your motivations, I don't feel very 
> comfortable with placing explicit atoms that are not supported by the 
> data.
> The fact that those atoms are present in high-resolution structure 
> does not mean that they are also present in low-resolution structure. 
> You can argue that adding these waters improves Rfree and you may 
> think of it as an improvement. However, as a counterargument one can 
> say that R-factor is a global metric that is unlikely to be sensitive 
> to adding/removing just one single molecule. Therefore, while adding 
> bulk of "structured" waters may be an improvement in general this 
> still does not mean that all the waters you add are true and good 
> ones. Say what if 70% of them are good and 30% are rubbish? In this 
> case still Rfree may improve because you add more good water than bad, 
> but adding bad ones is counterproductive anyway and introduces model 
> bias and thus must be avoided.
> All the best,
> Pavel
> On 11/17/14 1:33 AM, Guenter Fritz wrote:
>> Dear Pavel,
>> yes, such an exact prediction of ordered water molecules might be 
>> very helpful. I was sure that somebody else had this idea already.
>> I was playing around with a few datasets truncated a low resolution 
>> (3.5 - 4.0 A) and then compared Rwork/Rfree using an input model with 
>> and without water molecules. Clearly the water molecules had a large 
>> contribution in the refinement of these artificially truncated 
>> datasets. Sascha pointed me to an example in your paper from 2002:
>> Lunin, V.Y., Afonine, P. & Urzhumtsev, A.G. (2002) "Likelihood-based 
>> refinement. 1. Irremovable model errors.". Acta Cryst., A58, 270-282.
>> I had a look into the  literature to get an idea and found several 
>> programs evaluating the inner shell water molecules and some programs 
>> predicting water positions. I had a try only on a few programs. I 
>> found that a nice summary is given in the publication on an approach 
>> called WaterDock:
>> Ross GA, Morris GM, Biggin PC (2012) "Rapid and accurate prediction 
>> and scoring of water molecules in protein binding sites." PLoS One 
>> 7(3):e32036.
>> But before analyzing many structures and see whether it might work in 
>> general,  my aim is much simpler. I have high resolution structures 
>> of with water molecules and try to implement the ordered water 
>> molecules into the refinement of a protein complex at low resolution. 
>> My approach was maybe a bit of naive so far but I am sure there is 
>> good way to do that.
>> Best wishes, Guenter
>>> Hello,
>>> I tried this idea back in 2004. In a nutshell: using all (or 
>>> categorized subset of) structures in PDB we can learn about 
>>> distribution of structured water and given this knowledge we can 
>>> build an a priori contribution of scattering arising from such water 
>>> to the scattering of any given new structure or a structure at low 
>>> resolution (where the water is not visible in maps).
>>> Either I did not spend enough time on this or the idea wasn't 
>>> viable, but one way or another this did not work in my hands. I 
>>> think it may be worth revisiting this 10 years later! Perhaps I 
>>> would do it better now than back then!
>>> All the best,
>>> Pavel
>>> On 11/16/14 2:19 PM, Nathaniel Echols wrote:
>>>> I will leave it to others to debate the wisdom of this strategy, 
>>>> but to answer the purely technical question:
>>>> On Sun, Nov 16, 2014 at 2:06 PM, Guenter Fritz 
>>>> <guenter.fritz at uni-konstanz.de 
>>>> <mailto:guenter.fritz at uni-konstanz.de>> wrote:
>>>>     Is it possible to use protein and water atoms from the
>>>>     reference models to generate restraints for the low resolution
>>>>     refinement?
>>>> I don't think so.  You'll probably find it easier to refine the 
>>>> atoms separately, i.e. one run with reference model and the 
>>>> individual sites selection set to "not resname HOH", followed by a 
>>>> run with harmonic restraints on waters and selection "resname 
>>>> HOH".  Alternately, you could try applying harmonic restraints to 
>>>> the entire model, although I suspect that the waters and protein 
>>>> require different weights (or sigmas).
>>>> -Nat

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