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Re: [ccp4bb]: Monoclinic twinning?
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I don't think you have twinning. How do your scaling statistics vary
between P222 and P2 with each axis being the unique axis? If the
R-factors drop considerably from P222 to P2, then you most likely have P2
symmetry. If they only change by a little ([Flame retardent on] a
specific number is a topic of heated debate [Flame retardent off]), then
you have the higher symmetry of P222 and should re-evaluate the screw axes
by careful inspection of the appropriate zones for systematic absences.
This means actually going back to the raw images and not just the
Scalepack output. We had several cases where systematic absences were not
detected because of bleed over from the adjactent strong reflection.
Most likely what you are seeing in your monoclinic scaling is the fact
that the Beta angle is close to 90 degrees and Denzo/Scalepack does not
handle this very well. As you can see from your output for autoindexing
it is happy putting the orthorhombic Beta or the orthorhombic Alpha angle
supplement as the Monoclinic Beta angle (remember to keep your coordinate
system right handed). I am assuming from your Space Group that you are
using a=57, b=91,and c=112 in the orthorhombic setting.
If your crystal were truly twinned, then with a refined Beta=91 at
higher resolution your spots along h and l should start to streak and
become discrete. You could calculate the resolution at which overlapped
spots would separate using the refined crystal parameters, mosaicity, and
detector information (pixel size). I would also expect general mosaicity
to be artificially higher as the spots start to diverge a higher
resolution. Check the high resolution spots carefully for signs of two
maxima, which would be an indication of divergence.
As was posted earlier in the day, you need to be careful of convention.
You wrote your space group as P 21 2 21. Assuming you used increasing
axis length to denote your orthorhombic axis, your unit cell is a=57,
b=91, c=112, alpha=beta=gamma=90. This is a valid space group, but is
typically reindexed to P 21 21 2, which would make your axes a=112, b=57,
c=91, alpha=beta=gamma=90. You might want to try a careful reindexing and
On Wed, 5 Feb 2003, matthew.c.clifton.1 wrote:
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>*** CCP4 home page http://www.ccp4.ac.uk ***
>I may have come across an example of monoclinic twinning in my data that
>appears to be orthorhombic.
>I am working on a MAD data set that appears to be in the space
>group P21221. However, upon running the data through SOLVE, the electron
>density maps are very difficult if not impossible to follow even though
>the data set was to 2.4 angstroms. I thought that I had the wrong space
>group and I proceeded to process the data as monoclinic.
>During the indexing of the data as P2, a strange problem occurred. DENZO
>had problems with the identification of the correct lattice (they varied
>between data sets taken from the same crystal in the exact same
>Example indexing in P2:
>Peak_minus data set 57.38 91.51 112.37 90 90.24 90
>Inflection_minus data set 91.53 57.4 112.36 90 90.24 90
>The data from the inflection wavelength could be "corrected" such that it
>found the same lattice as the Peak_minus data set by adding ~200 more
>peaks to the indexing, but it changed the unit cell parameters to:
>57.15 91.36 111.06 90 91.04 90
>Following this, I decided to investigate the possibility of twinning. I
>ran the data through the CNS program detect_twinning where it output the
><|I|^2> / (<|I|>)^2 = 1.6711 (average value over all bins, where 2.0 is
>untwinned and 1.5 is for twinned).
>(<|F|>)^2 / <|F|^2> = 0.8602 (average value over all bins, where 0.785 is
>untwinned and 0.865 is twinned).
>When the data was processed through TRUNCATE, the Cumulative Intensity
>Distribution looked almost exactly like the example given on the CCP4
>website for a twinned crystal. The data appears to be clean with no large
>streaked reflections or the presence of a secondary lattice.
>Is the data truly twinned? If so, how is this happening geometrically? (I
>am having a hard time drawing a picture of this). The only example I can
>find that is similar is an abstract from the bioinformatics-structure
>conference in Jerusalem, Israel from November 17-21, 1996 (HiPIP II
>structure to 1.7 angstroms resolution from a twinned monoclinic crystal).
>Any suggestions on how to proceed from here would also be helpful.
>If not, why is all the data indicating that it may be twinned?
>Any suggestions or input would be appreciated.
>Thanks in advance,
Christopher L. Colbert, Ph.D.
Howard Hughes Medical Institute Phone: (214) 648 5002
University of Texas Southwestern Medical Center FAX: (214) 648 5095
5323 Harry Hines Boulevard
Dallas, TX 75390