I played with this (coded from scratch, both simple algorithm and a few
tweaks) for a couple of weeks for solving heavy atom substructures. With
perfect FAs it works well and quickly. With real delta-F's it didn't
work at all. Can't remember if I tried perfect delta-F's.
Probably SUPERFLIP is better than my quick implementation though.
Francis E Reyes wrote:
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
---------------------------------------------
Francis Reyes M.Sc.
215 UCB
University of Colorado at Boulder
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