[phenixbb] explicit solvent in low resolution refinement

Pavel Afonine pafonine at lbl.gov
Sun Nov 16 14:43:59 PST 2014


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,

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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