Hi all
I've been playing around with charge flipping for macromolecular
substructure determination with pretty promising results. I'm
particularly attracted to the fact that it solves structures in P1,
with no space group assumptions and curious how it would handle some
of the pseudosymmetry cases I've come into in my time.
I'd like to know if anyone's had experience with this method, and
open up the discussion with the following questions:
As the algorithm starts with completely random phases and charge
flips the map in P1, what is the importance of measuring (good or
any) anomalous signal at all (for the sole purpose of finding the
heavy atoms)? At first pass it would seem that just as long as you
have an incorporated heavy atom and the density of that region is
greater than delta, that this alone would be sufficient for locating
the position of the heavy atom. In other words just as long as your
heavy atom is sufficiently higher in contrast than your protein/rna it
would be a good enough criteria.
In the above regime, would the importance of measuring anomalous data
be more important for substructure refinement (via phaser, mlphare,
sharp, solve/resolve)?
Now to a more specific question for those who've had experience (or
maybe the authors are subscribed here):
Orthorhombic C2221 using SUPERFLIP heavy atoms are found with great
peakiness (before noise suppression: peakiness = 5, after noise
suppression peakiness >25, good separation of heavy atom peaks from
noise peaks in resulting pdb). Yet the space group check via the sym
operators is rather poor (overall agreement close to 100). My
interpretation is that the heavy atoms are found, but the space group
is wrong?
Thanks!
F
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Francis Reyes M.Sc.
215 UCB
University of Colorado at Boulder
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