Yuan Cheng wrote:
Eleanor Dodson wrote:
This phenonema doesnt necessarily mean you have lattice-tranlation
defects - pseudo translations are quite common with perfectly good
crystals.
Lattice translation defects usually imply your "crystal" has two or
more layered different crystals in the beam.. It can be best detected
by an analysis of the data statistics.
Eleanor
Yuan Cheng wrote:
Eleanor Dodson wrote:
You must have a pseudo translation vector of ~ 0.02 0.5 0.0
That relates solution 1 and 2, and 3 and 4.
That makes it hard to determine space group - there will be
absences along 0k0 because of the translation so the space group
could be P 2i 2 2i or P2i 21 2i
But which ever SG it is thedata with k odd will be weak, and that
means you will have a higher R factor.
Eleanor
Jerry McCully wrote:
Dear all:
I am currently refining a structure solved by MAD and
somehow the R factor got stuck around 30% with 2.2 resolution.
There are four molecules in one ASU. Two had very good
density map and the other two were not equally good.
I tried using NCS during refinement but it did not help
much.
Then I checked my data. Actually I found that there are
alternate layers of strong and weak reflections. THe crystal is
in a thin-plate shape with orthorombic space group.
Then I looked at my molecular replacement solution from Phaser
using my native data.
Actually phaser gave two sets of solutions, which showed
slightly different positions.
You can also see that there is a translation inside the same set
of solution.
SOLU SET RFZ=12.8 TFZ=21.4 PAK=0 LLG=452 RFZ=10.7 TFZ=47.9 PAK=0
LLG=1693 RFZ=13.0 TFZ=47.6 PAK=0 LLG=2791 RFZ=10.7 TFZ=46.1 PAK=0
LLG=4045
SOLU 6DIM ENSE ensemble1 EULER 184.052 0.185 175.770 FRAC
-0.49889 -0.00218 -0.00000
SOLU 6DIM ENSE ensemble1 EULER 225.116 0.167 134.696 FRAC
-0.47056 0.49706 0.00051
SOLU 6DIM ENSE ensemble1 EULER 359.333 31.677 180.633 FRAC
0.75769 -0.71475 -0.14004
SOLU 6DIM ENSE ensemble1 EULER 359.373 31.969 180.711 FRAC
0.73074 -0.21423 -0.14108
SOLU SET RFZ=12.8 TFZ=21.4 PAK=0 LLG=452 RFZ=10.7 TFZ=47.9 PAK=0
LLG=1693 RFZ=13.0 TFZ=47.6 PAK=0 LLG=2791 RFZ=10.7 TFZ=47.3 PAK=0
LLG=4042
SOLU 6DIM ENSE ensemble1 EULER 213.115 0.173 146.741 FRAC
-0.49931 -0.00269 0.00045
SOLU 6DIM ENSE ensemble1 EULER 248.173 0.254 111.665 FRAC
-0.47091 0.49661 0.00101
SOLU 6DIM ENSE ensemble1 EULER 359.399 31.602 180.578 FRAC
0.75808 -0.71455 -0.13980
SOLU 6DIM ENSE ensemble1 EULER 359.378 31.255 180.361 FRAC
0.78370 -0.21555 -0.13830
I remember there is a discussion in CCP4bb about the same
topic with the focus of pseudo-symmetry or translational
pseudo-symmetry. Can anybody give some troubleshooting
about my issue?
Thanks a lot and have a nice weekend,
Jerry McCully
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Hi Jerry,
I am having similar trouble with you. You might want to check out
this paper Acta Cryst.(2005) D61:67-74. It is about
lattice-tranlation defects and how to correct it. Hopefull it is
helpful!
Good Luck!
Yuan
Hi Eleanor,
Could you explain a little bit more about how to tell the
difference between pseudo-translational symmetry and lattice
translation defects? Thanks a lot!
Yuan
Hmm - that is hard.. pseudo translation is relatively harmless - you
have 2 or more molecules in the same orientation but in different
positions in the unit cell, and the structure factors they generate will
have some different properties. For instance the 0k0 in your case will
always have k=2n+1 weak because the translation is xt, 0.5,zt ( you can
work that out from a SF equation if you like!) And since the xt =
0.02, ie is rather small, and zt = 0, at low resolution all the hkl with
k=2n+1 will be weak.
use
hklview data.mtz and look at h0l then next level , next level etc and
you should see this effect..
The only problem it gives in is determining the spacegroup. But phaser
will usually sort that out as long as you let it test all SGs .
Lattice translation is effectively one form of twinning, you can
visualise it as a set of crystals where that lattice are aligned in 2
dimensions but there is slippage along the third. So each "reflection"
is in fact the sum of two or more intensities and the twinning analyses
should be valid. But as well you have the problem that some classes of
reflections are very weak, in the same way as a pseudo translation
affects the data.
And the twinning tests via moments, H test and Britten test are all
distorted by the weak/strong pattern so really the only effective test
is the L test, and that too can be badly distorted by anisotropy and
other defects.
Apparently it is often possible to recognise a lattice defect by looking
at the images, if you are good at that. Some classes of reflections will
be very streaky ( where there is an overlap between the different
crystal fragments) and others sharp. But once the data is integrated
that information is lost.
Does that help?
Eleanor
