[phenixbb] explicit solvent in low resolution refinement

Guenter Fritz guenter.fritz at uni-konstanz.de
Mon Nov 17 01:33:18 PST 2014

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 

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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