Hi,
In principle, when you solve a structure by molecular replacement with Phaser, you should end up with a reasonably compact assembly near the origin of the unit cell. However, I usually use coot to shuffle around the symmetry copies (one of my favourite features!) to make the most sensible arrangement, particularly when there are multimers with NCS symmetry.
Unfortunately, Phaser has had a bug in this feature for the past year or so, as Robbie Joosten kindly pointed out to us recently. We've now fixed this bug, and a corrected version of Phaser will appear soon in a new Phenix release and hopefully not too much later as a CCP4 update. In the meantime, it would be a good idea to check any molecular replacement solutions you generated in Phaser over the last while and choose better symmetry copies if the solution has ended up far from the origin.
Sorry for the trouble!
Best wishes,
Randy Read
Dear Paul,
Yes thank you. This was the best answer i think. Someone else already also suggested that also. Coot is very handy indeed.
(Would still be curious of knowing how to find the "closest to origin" copy otherwise - but this solves my problem)
Thanks to all who responded.
Cheers,
Tommi
On 13/12/2017 13:50, Kajander, Tommi A wrote:
> Hello,
>
> If someone could point this out would be very helpful... Wasnt there a simple script somewhere that would
> transfer coordinates close to origin - if they for some reason are not? Just cant find anything right away.
>
At the risk of not answering the question because it's not a simple script, my I recommend Coot?
File -> Open -> yourcoords.cif
Draw -> Cell & Symm -> Master Switch -> Yes
Show Unit Cells -> Yes
OK
Drag the View to the Origin # it's marked with an "O"
Middle-mouse click on an Symmetry-related Atom # that's close to the origin
Extensions -> Modelling -> Symm Shift Reference Chain Here
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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
