[phenixbb] explicit solvent in low resolution refinement

Nathaniel Echols nechols at lbl.gov
Sun Nov 16 14:19:58 PST 2014

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> 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).

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