These rings are nanocrystalline cubic ice (ice Ic, as opposed to the
"usual" ice Ih). It is an interesting substance in that noone has ever
prepared a large single crystal of it. In fact, for very small crystals
it can be hard to distinguish it from amorphous ice (or "glassy
water"). The three main rings that you see from ice Ic coincide almost
exactly with the centroids of the three main diffuse rings of glassy
water, and as the ice Ic crystals get smaller, the rings get fatter
(Scherrer broadening). You can even measure the size of the
crystallites by measuring the width of the rings. At the limit of 1-2
unit cells wide, the diffraction pattern of ice Ic powder looks almost
exactly like that of glassy water, so I suppose one could say that there
is a continuum of phases between the two.
And yes, there are crystals that "like" a certain mixture of cubic ice
and amorphous water in their solvent channels. Other's don't like it at
all. But I agree with JS below that the problem here is not the ice
rings. Probably overlaps? Best to look only at spots inside the 3.8A
circle until you figure out what is going on.
-James Holton
MAD Scientist
On 10/13/2011 11:20 PM, James Stroud wrote:
First of all, are you sure those are ice rings? They do not look typical. I
think you might have salt crystals from dehydration *before* freezing.
Otherwise, I think your freezing went well. Maybe try a humidity controlled
environment when you freeze.
Second, I'm not so sure the bad stats come from the contaminating rings. The
lattice seems to have some sort of problem, like a split lattice. You might be
able to tackle this problem by increasing your spot size or skewing it's shape
to compensate for the split. You need to investigate several images throughout
the run to see whether and how to manipulate your spot size. Sometimes, the
split lengthens the spots in the direction of the phi axis and you get lucky.
But I think the phi axis might be horizontal in this picture, which makes
things a little trickier. From one image, it is difficult to tell the pathology
of this crystal.
In principle, if you can accurately measure the most high-resolution spots
visible (which appear to be about 1.9 Å, guessing from your log file) then you
will have a pretty good data set, even with the contaminating rings.
Personally, I'd use Denzo for this data, but I don't know what is vogue with
the community right now. I still use O, so my tastes might be somewhat
antiquated.
James
On Oct 13, 2011, at 11:12 PM, ChenTiantian wrote:
Hi there,
I am processing a dataset which has bad ice rings (as you can see in the attach
png file).
I tried both XDS and imosflm, and got similar results, it seems that adding "
EXCLUDE_RESOLUTION_RANGE" cannot get rid of the effects of the ice rings.
the following is part of the CORRECT.LP which is the second attached file, you
can find more details there.
SUBSET OF INTENSITY DATA WITH SIGNAL/NOISE>= -3.0 AS FUNCTION OF RESOLUTION
RESOLUTION NUMBER OF REFLECTIONS COMPLETENESS R-FACTOR R-FACTOR
COMPARED I/SIGMA R-meas Rmrgd-F Anomal SigAno Nano
LIMIT OBSERVED UNIQUE POSSIBLE OF DATA observed expected
Corr
4.24 37152 5537 5545 99.9% 46.9% 52.7%
37150 2.48 50.8% 19.4% -28% 0.513 5136
3.01 55344 9002 9840 91.5% 62.7% 65.1%
55116 1.76 68.3% 48.1% -28% 0.520 7760
2.46 84636 12699 12703 100.0% 67.4% 84.7%
84634 1.55 73.0% 54.2% -19% 0.513 12104
2.13 97910 14743 14987 98.4% 254.5% 199.3%
97908 0.16 276.2% 4899.9% -23% 0.473 14037
1.90 110260 16846 16940 99.4% 299.2% 303.3%
110245 0.06 325.0% -99.9% -17% 0.422 15995
1.74 118354 18629 18744 99.4% 1062.0% 1043.6%
118317 -0.20 1156.4% -99.9% -13% 0.380 17414
1.61 122958 20193 20331 99.3% 967.5% 1571.1%
122868 0.10 1059.7% 987.3% -2% 0.402 18348
1.51 125075 21554 21794 98.9% 838.9% 1355.1%
124933 0.08 922.6% 1116.9% -1% 0.402 18977
1.42 72057 17042 23233 73.4% 640.8% 775.3%
70391 0.08 732.5% 826.7% -8% 0.425 10003
total 823746 136245 144117 94.5% 166.4% 166.7%
821562 0.40 181.1% 296.7% -15% 0.435 119774
Note that I/SIGMA of each resolution shell is<2.5, so how should I do to
process the dataset properly? Any suggestion about this super ice rings?
Thanks!
Tiantian
--
Shanghai Institute of Materia Medica, Chinese Academy of Sciences
Address: Room 101, 646 Songtao Road, Zhangjiang Hi-Tech Park,
Shanghai, 201203
<csrc.png><CORRECT.LP>
