[phenixbb] Maps from twinned data

Peter Zwart PHZwart at lbl.gov
Fri Feb 1 13:05:49 PST 2008


Hi Mary,

Can you try and download the latest cci_apps and recompute the maps
with phenix.refine?
I did make some updates since rc6 in the dewtinning code.

Cheers

Peter




2008/2/1, Mary Fitzgerald <mary.x.fitzgerald at gmail.com>:
> Peter-
> I've attached an image from coot.  I loaded my model and then a cns
> detwinned 3fo-2fc map (purple) and the 2fo-fc (blue) from phenix both are
> contoured at 1.5.  The 3fo-2fc is the only map have at the moment equivalent
> to the 2fo-fc model although it had waters in the model.  I have the
> symmetry brought up and there's not a symmetry related molecule in the area.
>  I've been working with this model quite a while and have never seen density
> there before.   It shows up in a couple of other spots as well with nothing
> appearing in the fo-fc maps, which I didn't show here.  It looks as if I'm
> missing part of my model in areas that there shouldn't be any model.
>
> Thanks,
> Mary
>
>
> On Feb 1, 2008 2:59 PM, Peter Zwart <PHZwart at lbl.gov> wrote:
> > Can you send a picture of the density and/or the data and model so I
> > can have a look.
> > The detwinning is done differently and for twin fractions of 0.5
> > something weird mihgt be happening.
> >
> > Thanks
> >
> > Peter
> >
> >
> >
> >
> > 2008/2/1, Mary Fitzgerald <mary.x.fitzgerald at gmail.com>:
> >
> >
> >
> > > I'm new to phenix and just installed Phenix 1.3 beta rc6.
> > >
> > > I've taken a data set that I've been refining in cns and am trying
> > > phenix.refine.  The data has a twinning fraction of 0.5.  I'm seeing
> what I
> > > think is odd in the 2mFobs-DFmodel.map.  If I'm reading the
> documentation
> > > correctly, this map should be detwinned (I also set
> > >
> refinement.twinning.detwin.map_types.aniso_correct=true), I
> > > see alot of extra density where there is no model, nor a symmetry
> related
> > > molecule in coot.  I don't see this extra density in my detwinned 2fofc
> cns
> > > maps.
> > >
> > > So, could the extra density I'm seeing be due to using a different
> program
> > > and it is detwinning the data differently.  The extra density is from
> the
> > > twin????
> > >
> > > Any input would be appreciated,
> > >
> > > Mary X. Fitzgerald
> > >  Postdoctoral Associate
> > > Arnold Lab
> > >
> > >
> > > _______________________________________________
> > > phenixbb mailing list
> > > phenixbb at phenix-online.org
> > > http://www.phenix-online.org/mailman/listinfo/phenixbb
> > >
> > >
> >
>
>
>



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