[phenixbb] partial model in autobuild?

Randy J. Read rjr27 at cam.ac.uk
Wed Dec 21 10:02:47 PST 2011

If your missing molecule is a 4th copy of the same thing then there's a good chance that molecular replacement will work after refining or rebuilding the first 3 copies, which should give you a better model. 

Alternatively you could average the density of the three copies in the initial model-phased map and search for a copy of that density, which should look more like the structure in the crystal. 

Finally, if this is related to the crystals we were discussing recently, the 4th copy should be related by a simple NCS translation to one of the first 3.

Good luck!

Randy Read

Randy J. Read

On 21 Dec 2011, at 01:01, "Yarrow Madrona" <amadrona at uci.edu> wrote:

> Hello,
> I would like to use autobuild to start from a partial model.  I have done
> Phaser EP with phases from MR.  I can see the fourth molecule but it is
> not well defined and I am not exactly sure where to place it. Is it
> possible to run autobuild from the partial model to fill in the fourth
> model?  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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