Good morning Randy, Setting aside the (always somewhat tricky) resolution limit choice, a useful consideration is embodied in equations 1,2 and 3 of https://scripts.iucr.org/cgi-bin/paper?bw0576 and the associated text ie consider the theoretical maximum of the anomalous differences. Without an absolute scale the differences greater than, say, 4 or 5 times the observed average value are unlikely. I feel sure we are all eager to know this possible improvement in Phaser that you are exploring. Greetings, John Emeritus Professor John R Helliwell DSc
> On 11 Oct 2020, at 14:17, Randy Read <rj...@cam.ac.uk> 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: > rj...@cam.ac.uk > 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/
