You could try the dials data processing - it tries to address the problems
of multiple lattices..
Eleanor
On 13 August 2018 at 08:59, Paul Adams <pdad...@lbl.gov> wrote:
> Hi Marcelo,
>
> based on this image it looks like you have multiple (two) lattices,
> which puts spots very close together. This could be a split crystal as
> Eleanor suggested, or a feature of the way the crystals grow. It seems
> unlikely that you’d be able to integrate these lattices well, given how
> close the spots are. You could try data collection with the detector pushed
> further back to increase spot separation (not an ideal solution). If the
> multiple lattices is something you see with all crystals then you may want
> to work on modifying crystallization conditions.
> Sometimes things can be very difficult to figure out. The Dicer
> structure (see Ian MacRae’s paper in Acta D: D63, 993-999, 2007) was a case
> where the a and b axes of the orthorhombic lattice were very similar in
> length and the crystals always grew with a pseudo-merohedral twinning that
> gave rise to nearly, but not quite, overlapped spots from the two lattices.
> It doesn’t look like you have a case like this, because the intensity
> statistics don’t suggest twinning. However, some of the tricks that you
> might use today on such crystals, such as raster scanning with a microbeam,
> might be helpful.
>
> Cheers,
> Paul
>
> > On Aug 12, 2018, at 9:57 AM, Randy Read <rj...@cam.ac.uk> wrote:
> >
> > I am sorry. I forgot to attach the image.
> >
> > Cheers
> >
> > Marcelo
> >
> > Em sáb, 11 de ago de 2018 às 18:31, Marcelo Liberato <
> marcelovliber...@gmail.com> escreveu:
> > Dear Eleanor,
> >
> > Thanks for you answer.
> > Indeed, there are clear ice rings in the images (example attached). So,
> I integrated again (P1, P2 and P222) excluding the resolution ranges
> 2.28-2.22 and 3.70-3.64. I am attaching the log files from aimless, MR and
> refmac for P2 (in two different cells) and P222 data.
> > I agree that MR seems very good (in all cases), but the final density
> maps are always bad. Maybe the data has problems that I am not dealing
> with.
> >
> > Kind regards
> >
> > Marcelo
> >
> > Em sáb, 11 de ago de 2018 às 16:04, Eleanor Dodson <
> eleanor.dod...@york.ac.uk> escreveu:
> > This MR looks good to me, but there are serious flaws with the data.
> Your secon moment plot from the aimless log has most spectacular spikes
> which are always a BAD THING, and the Wilson plot is not very smooth
> either..
> >
> > As Randy says, try to sort those problems out first.
> >
> > Then you have this message:
> >
> >
> > TRANSLATIONAL NCS:
> >
> > Translational NCS has been detected at ( 0.000, 0.500, 0.125).
> > A translation of 0.5 along B will generate pseudo-absences along b so
> you can be sure whether there is a scre axis or not..
> >
> > The space group is most likely orthorhombic - these indicators are
> pretty convincing for P2/mmm - so I dont know why you have chosen P21 as
> the spacegroup?
> >
> >
> > Scores for each symmetry element
> >
> > Nelmt Lklhd Z-cc CC N Rmeas Symmetry & operator (in
> Lattice Cell)
> >
> > 1 0.917 8.18 0.82 61009 0.298 identity
> > 2 0.883 7.85 0.78 100711 0.381 ** 2-fold l ( 0 0 1)
> {-h,-k,l}, along original k
> > 3 0.921 8.39 0.84 99542 0.355 *** 2-fold k ( 0 1 0)
> {-h,k,-l}, along original l
> > 4 0.920 8.26 0.83 99218 0.320 *** 2-fold h ( 1 0 0)
> {h,-k,-l}, along original h
> >
> > So my suggestions:
> > Sort out data problems
> >
> > Merge as P2/mmm
> >
> > Let MR search select the most likely spacegroup of the 8 possible.
> >
> > You cant even limit the b axis to be a screw axis .
> >
> > Your refinement behavior looks OK, but the maps will look bad with
> spurious reflections in the list..
> >
> > Eleanor
> >
> >
> >
> >
> >
> > On 10 August 2018 at 19:02, Eleanor Dodson <eleanor.dod...@york.ac.uk>
> wrote:
> > Actually Marcelo - Refinement to an R of 41% is pretty good for an MR
> solution!
> >
> >
> >
> > On 10 August 2018 at 18:42, Eleanor Dodson <eleanor.dod...@york.ac.uk>
> wrote:
> > Can you attach the refinement log?
> >
> > Eleanor
> >
> > On 10 August 2018 at 16:57, Marcelo Liberato <marcelovliber...@gmail.com>
> wrote:
> > Dear Randy,
> >
> > Thank you very much for answering. I followed your suggestions but,
> unfortunately, I couldn't get a reasonable electron density map after MR
> and refinement.
> >
> >
> > First I would look at the data to see if you have ice rings, because the
> peak in mean intensity and second moment of the intensity at about 2.25A
> resolution suggests an ice ring problem. If so, you should make sure you
> don't contaminate the data with spurious large intensities.
> >
> > Indeed, the data has ice rings. At first, I required imosflm to remove
> ice rings, but it didn't happened. So, I re-processed the data in different
> space groups removing the ice rings.
> >
> > Second, the statistics (e.g. the second moments plot after tNCS
> correction in Phaser) would be consistent with a scenario in which you have
> pseudosymmetry along with a twin operator that parallels the
> pseudosymmetry. If that's true, it's hard to be sure of the symmetry. For
> instance, if the structure really is monoclinic, can you be sure you chose
> the correct axis to be the 2-fold?
> >
> > I am not sure. However, I tried two possible axis to be the 2-fold and
> none of them gave me reasonable maps after MR and refinement.
> >
> >
> > Since you have a good model that gives clear MR solutions even in P21,
> you can probably process the data in P1 and solve it with 8 copies in the
> unit cell. Then you can look at the symmetry of the MR solution (e.g. in
> Zanuda) and see whether it obeys any higher symmetry than P1.
> >
> > I processed data in P1. After MR (with 8 copies in the ASU), it resulted
> in TFZ=11.6 and LLG=1434. But the map is still bad and high Rwork and Rfree.
> > According to Zanuda, the data should be P21:
> > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
> > | >> 4 | P 1 21 1 | 68.6868 | 0.6289 | 0.5487 | 0.5523 |
> > ---------------------------------------------------------------------
> > | 1 | P 1 | 69.4151 | 0.6171 | 0.5471 | 0.5559 |
> > | 4 | P 1 21 1 | 69.3810 | -- | 0.5482 | 0.5442 |
> > | 11 | P 21 21 21 | 52.0271 | -- | 0.6107 | 0.6178 |
> > ---------------------------------------------------------------------
> > | << 4 | P 1 21 1 | 69.3810 | -- | 0.5482 | 0.5442 |
> > ---------------------------------------------------------------------
> > I processed in P21 using two different unit cells, and MR resulted in
> TFZ=20.8 and LLG=511, and TFZ=56 and LLG=2867. However, again, no good maps
> and statistics.
> >
> > Best regards
> >
> > Marcelo Liberato
> >
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> >
> >
> >
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> >
> > <image 1.jpg>
>
> --
> Paul Adams
> Division Director, Molecular Biophysics & Integrated Bioimaging, Lawrence
> Berkeley Lab
> Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley
> Lab
> Adjunct Professor, Department of Bioengineering, U.C. Berkeley
> Vice President for Technology, the Joint BioEnergy Institute
> Laboratory Research Manager, ENIGMA Science Focus Area
>
> Building 33, Room 347
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