[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
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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