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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> 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
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