Hi,
please post the pointless table "Analysing rotational symmetry in lattice
group P 6/m m m". This gives a quite clear information about the
presence/absence of rotational symmetry axes.
Look at at the following example
Analysing rotational symmetry in lattice group P 6/m m m
----------------------------------------------
<!--SUMMARY_BEGIN-->
Scores for each symmetry element
Nelmt Lklhd Z-cc CC N Rmeas Symmetry & operator (in Lattice
Cell)
1 0.936 9.71 0.97 8676 0.077 identity
2 0.936 9.74 0.97 12213 0.071 *** 2-fold l ( 0 0 1) {-h,-k,l}
3 0.055 1.58 0.16 12097 0.514 2-fold k ( 0 1 0) {-h,h+k,-l}
4 0.056 1.74 0.17 12146 0.495 2-fold h ( 1 0 0) {h+k,-k,-l}
5 0.056 1.73 0.17 12274 0.505 2-fold ( 1-1 0) {-k,-h,-l}
6 0.055 1.61 0.16 12238 0.521 2-fold ( 2-1 0) {h,-h-k,-l}
7 0.056 1.69 0.17 12148 0.495 2-fold (-1 2 0) {-h-k,k,-l}
8 0.056 1.71 0.17 12056 0.511 2-fold ( 1 1 0) {k,h,-l}
9 0.248 6.35 0.64 24331 0.326 3-fold l ( 0 0 1)
{k,-h-k,l}{-h-k,h,l}
10 0.245 6.32 0.63 24629 0.327 6-fold l ( 0 0 1)
{h+k,-h,l}{-k,h+k,l}
Here, the 2-fold symmetry is just as good as the identity, and all the other
symmetries are insignificant, with one exception: there is a pseudo-3fold that
together with the true 2-fold gives a pseudo-6fold. So the true space group is
P2 (or P2_1) but it has 3-fold NCS.
I have seen even more interesting cases, where the CC was 0.8 to 0.9 for some
rotational elements - but even such a seemingly high CC was significantly lower
than the CC for the identity.
So my advice is: look at this table, and compare the CC values with that of the
identity operation.
Two caveats are:
1) a CC may be lower than the identity, due to radiation damage (but that must
then be quite significant)
2) a CC may be high, but still not mean true crystallographic symmetry, if
there is twinning
Finally, a different topic: Rmerge and Rmeas refer to precision of unmerged
data, and their values have no immediate relation to I/sigma, a precision
indicator for the merged data (in this table). So when somehow trying to
compare these values, you are comparing apples to oranges - but this is
meaningless.
HTH,
Kay
On Wed, 7 May 2014 18:26:24 +0100, <Rain Field> <rainfiel...@163.com> wrote:
>Hi all,
>I have a 360 degree data set collect on home beam.
>I used XDS to integrate the frames in P1.
>I progressively merge the data from P1 to P2 or P1 to P3 in XDS and attach the
>log below.
>The cell looks like P3 and pointless suggest P6. But the Rmerge and Rmeas are
>much higher than normal at I/sigmaI=2.
>I think P1 might be the true space group. But the Rpim reported by aimless
>seems high in the high resolution shell. Why is that?
>Thanks!
>
> LATTICE- BRAVAIS- QUALITY UNIT CELL CONSTANTS (ANGSTROEM & DEGREES)
> REINDEXING TRANSFORMATION
> CHARACTER LATTICE OF FIT a b c alpha beta gamma
>
> * 31 aP 0.0 62.5 82.5 82.6 60.1 89.9 90.0 -1
> 0 0 0 0 -1 -1 0 0 -1 0 0
> * 44 aP 0.2 62.5 82.5 82.6 119.9 90.1 90.0 1
> 0 0 0 0 1 1 0 0 -1 0 0
> * 41 mC 0.6 143.1 82.5 62.5 90.0 90.1 90.0 0
> 1 -1 0 0 -1 -1 0 -1 0 0 0
> * 30 mC 0.7 82.5 143.1 62.5 89.9 90.0 90.0 0
> -1 -1 0 0 1 -1 0 1 0 0 0
> * 35 mP 1.0 82.5 62.5 82.6 90.1 119.9 90.0 0
> -1 -1 0 -1 0 0 0 0 1 0 0
> * 40 oC 1.2 82.5 143.1 62.5 89.9 90.0 90.0 0
> -1 -1 0 0 -1 1 0 -1 0 0 0
> * 20 mC 2.6 142.9 82.6 62.5 90.0 90.0 90.1 0
> -2 -1 0 0 0 -1 0 1 0 0 0
> * 23 oC 3.3 82.6 142.9 62.5 90.0 90.0 89.9 0
> 0 1 0 0 -2 -1 0 1 0 0 0
> * 25 mC 3.3 82.6 142.9 62.5 90.0 90.0 89.9 0
> 0 1 0 0 -2 -1 0 1 0 0 0
> * 22 hP 3.5 82.5 82.6 62.5 90.1 90.0 119.9 0
> 1 1 0 0 -1 0 0 1 0 0 0
> 37 mC 249.8 176.5 62.5 82.5 90.0 117.8 69.3 1
> -2 0 0 1 0 0 0 0 1 1 0
> 42 oI 250.0 62.5 82.5 156.1 90.0 113.6 90.0 -1
> 0 0 0 0 -1 -1 0 1 -1 1 0
> 39 mC 250.6 176.4 62.5 82.6 90.0 117.9 69.2 1
> -2 -2 0 1 0 0 0 0 0 1 0
> 33 mP 434.8 62.5 82.5 82.6 119.9 90.1 90.0 1
> 0 0 0 0 1 1 0 0 -1 0 0
> 34 mP 435.2 62.5 82.6 82.5 119.9 90.0 90.1 -1
> 0 0 0 0 1 0 0 0 -1 -1 0
> 32 oP 435.4 62.5 82.5 82.6 119.9 90.1 90.0 1
> 0 0 0 0 1 1 0 0 -1 0 0
> 21 tP 437.6 82.5 82.6 62.5 90.1 90.0 119.9 0
> 1 1 0 0 -1 0 0 1 0 0 0
>
>
>
>P1:
> 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 CC(1/2) Anomal SigAno Nano
> LIMIT OBSERVED UNIQUE POSSIBLE OF DATA observed expected
> Corr
>
> 8.45 4500 1165 1288 90.5% 2.2% 2.4%
> 4498 51.19 2.6% 99.9* 10 0.838 1030
> 6.27 7174 1844 1872 98.5% 3.1% 3.0%
> 7173 35.92 3.6% 99.9* 11* 0.906 1671
> 5.20 9009 2288 2324 98.5% 4.5% 4.3%
> 9008 26.88 5.2% 99.8* 4 0.835 2168
> 4.55 10597 2686 2744 97.9% 5.2% 5.2%
> 10595 22.65 6.0% 99.7* -2 0.776 2557
> 4.09 12051 3051 3147 96.9% 7.5% 7.5%
> 12048 16.93 8.7% 99.4* 2 0.779 2915
> 3.75 12740 3226 3342 96.5% 14.8% 14.5%
> 12738 9.37 17.1% 98.2* 1 0.760 3078
> 3.48 14344 3631 3738 97.1% 22.2% 22.2%
> 14342 6.36 25.7% 95.8* 0 0.785 3471
> 3.26 15079 3813 3948 96.6% 47.3% 48.5%
> 15076 2.99 54.8% 83.7* -1 0.714 3655
> 3.08 14088 3797 4242 89.5% 99.7% 105.6%
> 13945 1.30 116.0% 58.6* -2 0.636 3133
> total 99582 25501 26645 95.7% 7.7% 7.9%
> 99423 14.49 9.0% 99.9* 1 0.765 23678
>
>P2:
> 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 CC(1/2) Anomal SigAno Nano
> LIMIT OBSERVED UNIQUE POSSIBLE OF DATA observed expected
> Corr
>
> 8.45 4499 638 711 89.7% 2.5% 2.7%
> 4497 63.58 2.8% 100.0* 16* 0.892 534
> 6.27 7172 986 993 99.3% 3.5% 3.5%
> 7172 46.06 3.7% 99.9* 10 0.948 872
> 5.20 8963 1202 1213 99.1% 4.9% 4.9%
> 8963 35.19 5.3% 99.9* 2 0.849 1101
> 4.55 10598 1413 1427 99.0% 5.8% 5.9%
> 10598 29.79 6.2% 99.9* -5 0.781 1308
> 4.09 12047 1608 1630 98.7% 8.5% 8.4%
> 12047 22.42 9.1% 99.6* -7 0.758 1500
> 3.75 12672 1687 1721 98.0% 16.2% 16.0%
> 12672 12.64 17.4% 98.9* 0 0.753 1591
> 3.48 14380 1918 1925 99.6% 24.7% 24.5%
> 14380 8.50 26.5% 97.9* -1 0.806 1806
> 3.26 15077 2011 2024 99.4% 51.5% 53.6%
> 15077 4.05 55.4% 90.8* -2 0.713 1907
> 3.08 14130 2055 2169 94.7% 109.3% 117.3%
> 14076 1.71 118.1% 73.6* -4 0.624 1799
> total 99538 13518 13813 97.9% 8.6% 8.8%
> 99482 18.92 9.2% 99.9* -2 0.768 12418
>
>P3:
> 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 CC(1/2) Anomal SigAno Nano
> LIMIT OBSERVED UNIQUE POSSIBLE OF DATA observed expected
> Corr
>
> 8.45 4507 394 429 91.8% 2.8% 3.0%
> 4506 78.31 2.9% 100.0* 22* 0.920 393
> 6.27 7171 621 621 100.0% 3.8% 3.7%
> 7171 56.42 3.9% 100.0* 19* 1.021 621
> 5.20 8953 769 774 99.4% 5.2% 5.1%
> 8953 43.07 5.4% 99.9* 4 0.886 769
> 4.55 10586 907 911 99.6% 6.1% 6.2%
> 10586 36.58 6.4% 99.9* -1 0.774 907
> 4.09 11997 1033 1045 98.9% 8.9% 8.8%
> 11997 27.69 9.3% 99.8* -2 0.768 1033
> 3.75 12620 1087 1112 97.8% 16.8% 16.6%
> 12620 15.75 17.5% 99.4* 0 0.777 1087
> 3.48 14358 1240 1240 100.0% 25.7% 25.6%
> 14358 10.50 26.9% 98.5* -4 0.776 1240
> 3.26 15023 1302 1306 99.7% 52.5% 55.0%
> 15023 5.11 54.9% 94.1* 1 0.718 1301
> 3.08 14198 1358 1410 96.3% 113.0% 122.5%
> 14162 2.12 118.7% 79.3* -7 0.617 1263
> total 99413 8711 8848 98.5% 9.0% 9.2%
> 99376 23.01 9.4% 100.0* 0 0.777 8614
>
>P1(aimless)
> Overall InnerShell OuterShell
>Low resolution limit 19.82 19.82 3.46
>High resolution limit 3.20 8.47 3.20
>Rmerge (all I+ and I-) 0.071 0.022 0.561
>Rmeas (all I+ & I-) 0.082 0.026 0.649
>Rpim (all I+ & I-) 0.041 0.013 0.326
>Total number of observations 90529 4500 18945
>Total number unique 22976 1165 4789
>Mean((I)/sd(I)) 16.1 53.6 2.5
>Mn(I) half-set correlation CC(1/2) 0.999 0.999 0.806
>Completeness 97.6 91.4 97.0
>Multiplicity 3.9 3.9 4.0
