On Sat, May 22, 2010 at 3:23 PM, Francis E Reyes <[log in to unmask]> 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

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Francis Reyes M.Sc.
215 UCB
University of Colorado at Boulder

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