Another reason why charge flipping may not work so well with real anomalous differences is that the data tend to be rather incomplete, for example all the centric reflections are missing. This degrades the quality of the resulting maps, which is more serious if you are modifying low densities than when you are just searching for peaks.
George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582 On Mon, 24 May 2010, George M. Sheldrick wrote: > I have also played with charge flipping and my experience was the same as > Kevin's. Michael Woolfson once said that all 'direct' methods work fine with > perfect data. The method requires expansion of the data to P1 which seems > to degrade the quality of the solution; when the data are noisy, as is > usually the case with real anomalous differences, the space group can be a > useful constraint, as is the number of sites expected. If necessary one > can easily run the usual programs in all potential space groups. For the > solution of small molecule structures using atomic resolution (say 0.9A) > native data, the data are much less borderline and charge flipping in P1 > is a good way to explore phase space. > > George > > Prof. George M. Sheldrick FRS > Dept. Structural Chemistry, > University of Goettingen, > Tammannstr. 4, > D37077 Goettingen, Germany > Tel. +49-551-39-3021 or -3068 > Fax. +49-551-39-22582 > > > On Mon, 24 May 2010, Kevin Cowtan wrote: > > > 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 > > > > > > gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D > > > > > > 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D > > > > > >
