I will look for examples but in practice I try to include rather than exclude data. (In fact follow the shelxd/e protocol slavishly allowing its automatic selection of data cutoff) When choosing a resolution cut off I think it is important to appreciate that the best test for correctness is the density modification step for selection of the hand. And at that stage higher resolution helps. Near random starting phases improve rapidly with density mod. Cycles. The anomalous signal has an associated SD so isn’t that used to weight down the less reliable high res terms. Will look out some old data sets for you... Eleanor
On Sun, 11 Oct 2020 at 14:17, Randy Read <[email protected]> wrote: > Dear members of the BBs, > > When determining the anomalous substructure as part of SAD phasing, one of > the most important parameters can be the choice of resolution limit for the > data provided to the substructure determination algorithm. Extending to > too high resolution can hamper the search by introducing too much noise. > The resolution limit is varied internally in phenix.hyss, but is provided > as a parameter to SHELXD. There are various rules of thumb that people use > to make a first choice of resolution limit, such as half-dataset anomalous > correlation or the average precision of the anomalous differences, or even > just adding 0.5 to dmin. > > We’re currently exploring some alternative measures and we would like to > test them on a significant number of relevant test cases. It turns out > that a large proportion of SAD data deposited in the PDB have such good > signal-to-noise that substructure determination succeeds with a wide > variety of parameters, so we’ve only collected a few cases so far. > > It would be great if you could let us know of cases that you’re aware of, > where substructure determination succeeds with the right choice of > resolution limit but fails with the full resolution range of data. Of > course, these have to be cases where the diffraction data have been > deposited at the PDB or otherwise been made available. We prefer data for > which the intensities, and not just the amplitudes, are available, but we > won’t be too picky if that would limit the number of examples too much! > > If you email me directly, I’ll post a summary to the BBs. > > Thanks! > > Randy Read > > ----- > Randy J. Read > Department of Haematology, University of Cambridge > Cambridge Institute for Medical Research Tel: +44 1223 336500 > The Keith Peters Building Fax: +44 1223 > 336827 > Hills Road E-mail: > [email protected] > Cambridge CB2 0XY, U.K. > www-structmed.cimr.cam.ac.uk > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a > mailing list hosted by www.jiscmail.ac.uk, terms & conditions are > available at https://www.jiscmail.ac.uk/policyandsecurity/ > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
