[phenixbb] phaser spacegroup within phenix

John M. Berrisford jmb at mrc-mbu.cam.ac.uk
Wed Jun 16 01:02:56 PDT 2010

Hi Nat

I don't think its a bug, just phaser getting a little bit confused. Phaser ran in both P2 and P21 using the phenix default, not P21 - the space group of the mtz. This default is probably the right thing to do if you don't know the space group of your crystal, but then you wouldn't have scaled the mtz in P21.

In my case the reason phaser failed to find a solution is that the P2 solution had a higher initial LLG than the P21 solution while finding the first copy of 4 in my A.U.. So phaser picked P2 to continue the molecular replacement and subsequently stopped due to clashes during packing.


On Tue, Jun 15, 2010 at 8:45 AM, John M. Berrisford
<jmb at mrc-mbu.cam.ac.uk>wrote:

> >  I have an mtz processed in P21 and when I load it into the phenix phaser
> >  GUI it tells me its P21 (P 1 21 1) and gives me no other options. However,
> >  when I run the molecular replacement job it decides that the space group
> >  could be either P2 or P21 and runs both - which in my case runs in P2 and
> >  gives a partial solution, not the full solution I would expect in P21. A bit
> >  annoying as I know my space group is actually P21.
> >  After a few minutes of head scratching, the only way I found to fix it to
> >  run in P21 is to enter the "other settings" menu and select "none" within
> >  "alternative space groups". I guess this is what your suppose to do, but its
> >  not obvious.
Point taken - I'll move this to the main window (and label it more clearly -
sorry).  The result you're describing sounds like it might be a bug, though;
shouldn't Phaser try P21 as well and get the full solution, instead of
settling for P2?  This is what I would expect for the default behavior.


John Berrisford

Medical Research Council
Mitochondrial Biology Unit
Wellcome Trust / MRC Building
Hills Road
WEB: www.mrc-mbu.cam.ac.uk
Tel: +44 1223 252882

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