[phenixbb] Quest for resolution-sensitive substructure determination cases

Randy Read rjr27 at cam.ac.uk
Sun Oct 11 06:17:21 PDT 2020

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.


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: rjr27 at cam.ac.uk
Cambridge CB2 0XY, U.K.                              www-structmed.cimr.cam.ac.uk

More information about the phenixbb mailing list