[phenixbb] Phaser problems

Randy J. Read rjr27 at cam.ac.uk
Sun Dec 18 00:07:31 PST 2011

It sounds like Phaser is finding the same solution but, for some reason, the packing step is not choosing symmetry related copies that pack together well. It's possible that recent changes to add new features have also added new bugs to this step!

Could you send the files needed to reproduce this bug to me (offline) so we can look into it?


Randy Read

Randy J. Read

On 18 Dec 2011, at 00:55, "Yarrow Madrona" <amadrona at uci.edu> wrote:

> Hello,
> Lately I have been having some trouble with phaser MR. For some reason
> even if I get a complete solution, it involves molecules from two
> different unit cells and it one case it picked up a symmetry related
> molecule as a crystallagraphic dimer.
> Recently I re-ran jobs from a sucessful run (over a year ago) in Phaser
> 2.1.4 where I get 4 molecules in the asymetric unit with plausable
> contacts that refined very well.
> Recently, however, I have re-run the job with the same search molecule and
> settings (all default). Although I get a solution, it involves molecules
> apparently from two asymetric units. The dimers formed are not the same
> contacts as what was seen in the earlier phaser run with Phaser 2.1.4.
> However if you turn on the symetry related molecues the tight
> crystallagraphic dimer seen previously shows up between one molecule and a
> symmetry mate.
> Has anyone had experiences like these recently with phaser? BTW my search
> model is 99% identical to my molecule (only one residue difference).
> Thanks.
> -Yarrow
> -- 
> Yarrow Madrona
> Graduate Student
> Molecular Biology and Biochemistry Dept.
> University of California, Irvine
> Natural Sciences I, Rm 2403
> Irvine, CA 92697
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