Hello Fred,
Thank you for the response.
I have made a mistake in the twin refinement settings (see the other email) and
the best R & Rfree values I obtained were from the twin refinement of structure
factor amplitudes, which is about 1% less than the twin refinement of
intensities.
I have not used Bhat's omit maps before. I will give it a shot and see how it
may improve my model building.
Best,
Peter
> Date: Wed, 13 Oct 2010 17:35:09 +0200
> From: frederic.velli...@ibs.fr
> To: pc...@hotmail.com
> Subject: Re: [ccp4bb] Twin - Data reduction and refinement in Refmac
>
> Peter Chan wrote:
> > Hello All,
> >
> > I am a graduate student working on my first merohedrally twinned data
> > set. Like a few, I am a bit intimidated by it. After some trial and
> > error with the help of some online resources and ccp4bb posts, I seem
> > to have solved the structure. However, I am still unsure about some of
> > the steps taken.
> >
> > Background:
> > My dataset was processed to 1.95 A in XDS, the apparent space group is
> > P622 (96 A, 96 A, 92 A, & 90, 90, 120). Various tests indicate that I
> > have a twinned dataset. The Rsym of the data when processed in a lower
> > symmetry space group (i.e. P6, P321 and P312) suggest that the real
> > space group may be P6 because its Rsym is lower by ~1-2%. The screw
> > axis could not be unambiguously identified from systematic absences.
> > Molecular replacement by Phaser returned a solution in P6(5) with 2
> > molecules in the asymmetric unit. This was refined in Refmac with the
> > twin option to R & Rfree of 22% and 25%. The twin fractions are 47%
> > and 53%.
>
> Usually the R and Rfree are slightly higher with twin refinement than
> with untwinned data; these figures look satisfactory to me.
>
> >
> > My questions and concerns:
> > - First and foremost, is there a chance that I may have processed the
> > data in the wrong space group (or wrongly deduced the data in the
> > right space group)?
> >
> > - Should the diffraction data be merged or unmerged during the twin
> > refinement in Refmac? The current dataset is fully merged (repeated
> > measurements, Friedel pairs & symmetry related reflections). Would
> > there be an improvement in the twin refinement if some of them are
> > kept unmerged?
> >
> > - Should the twin refinement be performed on the intensities or
> > structure factor amplitudes? I have tried both (using the same set of
> > Rfree flags): With intensities, the R/Rfree are 22%/25% and twin
> > fractions are 47%/53%. With amplitudes, the R/Rfree are 25%/29% and
> > twin fractions are 44.6%/55.4%. The resulting electron density maps
> > are not significantly different, however. I don't understand why the
> > statistics vary so significantly.
>
> I would use the refinement that gives the lower R / Rfree (no questions
> asked).
>
> >
> > - During the model building, the electron density map appears to be
> > 'weak'. Rebuilding some surface loops (by first deleting them,
> > refining the omit structure, and remodeling into the difference map)
> > which initially has some 2Fo-Fc density becomes tricky because there
> > is not much density left in the refined omit structure. Was the
> > initial densities purely a result of model bias or is this related to
> > the twinning of the crystal? Could this also be because Refmac outputs
> > a differently weighed 2Fo-Fc map (if I recall correctly) during twin
> > refinement?
>
> Have you tried Bhat's Omit maps as well? Possible to compute using
> either sfcheck or omit (the latter is not in ccp4bb).
>
> >
> > I would be very grateful for any help, comments and suggestions.
> >
> > Best,
> > Peter Chan
>
