Hi Antonio,
My question is how can I determine which water is needed, which is not
needed?
may be this will give you some clues - here are the approximate criteria
for water picking that are used in automatic water picking and
refinement in phenix.refine:
1) peak at mFo-DFc map is higher than ~3sigma, and
2) peak center is within a hydrogen bond to another atom (water or
macromolecule), and
3) peak has approximately the same shape as a water molecule would have
at this resolution and local environment, and
4) peak at 2mFo-DFc is higher than ~1.5 sigma,
after a round of coordinate and B-factor refinement,
the criteria (2-3-4) are still ok, and
5) refined B-factor of newly placed water is meaningful (didn't jump to
large value), otherwise a water is deleted.
There are a few other technical tricks to make this process robust and
efficient at high resolution, higher than ~1.2A or so, but this is, I
guess, beyond of what you were asking about.
Pavel.
