[phenixbb] difficult phasing problem

Randy Read rjr27 at cam.ac.uk
Thu Aug 9 14:54:48 PDT 2012

Dear Ian,

If you have a recent version of Phenix, then Phaser should automatically account for the effects of tNCS, so that shouldn't be the problem.  If you don't have a recent version then I strongly recommend updating to the latest stable build or an even more recent nightly build.

If you do have a recent version, then highly negative LLG values imply that your model agrees much more poorly with the data than Phaser is expecting.  Are you telling Phaser the truth about the sequence identity of your template?  (Doing homology modeling doesn't improve the accuracy enough to justify changing the sequence identity.)  Have you specified the composition correctly?  Are you certain of the space group?

If none of this helps, then you could send me a Phaser logfile (off-line) and I could see whether there are any hints in there.

Good luck!


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

On 9 Aug 2012, at 22:44, Ian Slaymaker wrote:

> I am trying to solve the structure of a ~30kd monomeric protein for which we have 2.5A diffraction data, and a search model with ~65 % similarity (i have tried, homology models of this and others, as well as using sculpter to build several variations of core search models). I have tried all my possible space groups and a huge range of parameters, and mr_rosetta to rebuild some of my better (but still bad) MR solutions. My LLG is persistently negative (<-1000), which may be due to translational noncrystallographic symmetry which was identified by xtriage. We have unfortunatly been unable to phase this data with selmet SAD, so I am looking for some other MR things to try. Any suggestions for working with tNCS (if this is really the problem) would be much appreciated.    _______________________________________________
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