[phenixbb] Recent improvements in Phaser for systematically weak data

Randy Read rjr27 at cam.ac.uk
Fri Dec 9 06:57:11 PST 2016

Dear all,

Between the last official release of Phenix (version 1.11.1-2575, released on 26 October) and a recent CCP4 update (7.0.023 released on 23 November), we fixed a problem in which the fast rotation function was not properly accounting for the effect of measurement errors in intensities.  Under many circumstances (i.e. with well-measured data to the resolution needed to solve the structure by MR), the change is not noticeable.  However, if you have systematically weak data (particularly from high levels of anisotropy or potentially from the effects of translational non-crystallographic symmetry), the fix can mean the difference between failing to solve the structure, because the correct orientation has not been generated, or solving it with a default run of Phaser.

We recommend that anyone trying to solve a structure with substantial anisotropy (anisotropic deltaB of 50 A^2 or greater) and/or translational NCS should update to a newer version of either package.  If you're using CCP4, you should get the latest update, because there was a problem with the version of coot distributed with the 7.0.023 update.  If you're using Phenix, you should get a recent nightly build, i.e. dev-2608 or something even newer.  Please note that you want to provide data to Phaser in the form of intensities rather than amplitudes to get the best results for such data!

So far, I've found 3 of our test cases where this makes a real difference, but I would be interested in hearing from anyone who finds that this makes a difference for other cases.

Best wishes,

Randy Read

Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research      Tel: + 44 1223 336500
Wellcome Trust/MRC 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

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