[phenixbb] Maps from twinned data

Mary Fitzgerald mary.x.fitzgerald at gmail.com
Mon Feb 4 10:05:59 PST 2008


I just tried the latest cci_apps and re-ran the refine job.  The new version
seems to clear up the problem.

Thanks,

Mary

On Feb 1, 2008 4:05 PM, Peter Zwart <PHZwart at lbl.gov> wrote:

> 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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