For what it's worth, I've been told that Rmerge was used originally, in
the pre-cryo few images per crystal age, to indicate the R-factor for
merging data collected from multiple crystals. Isym is calculated
identical but refers to data collected from a single crystal.
To be honest I'm not sure if this reflects history or somebody trying
to make something out of nothing but I've been using Rsym ever since.
Bart
Phil Evans wrote:
I've never been able to discover any difference between Rsym & Rmerge
Phil
On 21 Jan 2010, at 18:34, james09 pruza wrote:
Dear All CCP4bbers,
Please help me in finding *R-sym I *(observed), *R-merge I*(obseved), *R-Free
Error i*n the data provided below. If I am not wrong, Can anyone suggest me
the difference between R-sym and R-merge?
Thanks in advance for the help.
James*
*
R-values of internal consistency :
======== --------------------
(Anomalous scaling counts I+ and I- as separate hkl.)
R-merge ( sum |Ij-<I>| / sum |<I>| ) = 23.4 % ( 21.57 % for Fsq > 0)
where <I>=sum(Ij)/N, j=1...N,
calculated from 188629 observations of 60655 /+//-/ reflexions
- dito within user-defined resolution: 23.4 %
calculated from 188182 observations of 60508 /+//-/ reflexions
Sigma-weighted R-merge :
( sum wj*|Ij-<I>| / sum |<I>| ) = 19.1 %
where <I>=sum(wj*Ij), j=1...N,
with sum(wj)=1,
calculated from 133636 observations of 60655 /+//-/ reflexions
- dito within user-defined resolution: 19.1 %
calculated from 133323 observations of 60508 /+//-/ reflexions
Multiplicity of accepted measurements for unique reflexions, and
completeness C
in equal-volume shells (on average 4161 possible unique reflexions each):
Shell- 1* 2* 3* 4* 5-6* 7-8* 9-12* 13-16* >16* total
C[%]
limits [A] ----- ----- ----- ----- ----- ----- ----- ----- ----- -----
----
inf. - 30.0 excluded... (but see right below)
0.0
30.0 - 6.46 221 878 805 1620 597 0 0 0 0 4121
95.1
6.46 - 5.13 73 659 726 1850 840 0 0 0 0 4148
98.9
5.13 - 4.48 80 687 841 1823 712 0 0 0 0 4143
99.1
4.48 - 4.07 72 673 802 1778 772 0 0 0 0 4097
99.3
4.07 - 3.78 94 595 735 1862 831 0 0 0 0 4117
99.4
3.78 - 3.56 108 563 738 1883 856 0 0 0 0 4148
99.7
3.56 - 3.38 81 519 689 1968 886 0 0 0 0 4143
99.8
3.38 - 3.23 49 465 731 1976 877 0 0 0 0 4098
100.0
3.23 - 3.11 58 485 772 1950 875 0 0 0 0 4140
100.0
3.11 - 3.00 39 457 768 1944 832 0 0 0 0 4040
98.8
- - - - - - ----- ----- ----- ----- ----- ----- ----- ----- ----- -----
----
* 30.0 - 3.00 875 5981 7607 18654 8078 0 0 0 0 41195
99.0
----------- ----- ----- ----- ----- ----- ----- ----- ----- ----- -----
----
Below specified lower-resolution limit :
inf. - 30.0 0 1 0 0 0 0 0 0 0 1
Beyond specified high-resolution limit :
3.00 - 2.99 0 37 25 51 9 0 0 0 0 122
Same multiplicities as relative percentages [%] and <average multiplicity>
(total measured unique reflexions in each shell = 100.%)
30.0 - 6.46 5.4 21.3 19.5 39.3 14.5 . . . .
<3.38>
6.46 - 5.13 1.8 15.9 17.5 44.6 20.3 . . . .
<3.67>
5.13 - 4.48 1.9 16.6 20.3 44.0 17.2 . . . .
<3.58>
4.48 - 4.07 1.8 16.4 19.6 43.4 18.8 . . . .
<3.61>
4.07 - 3.78 2.3 14.5 17.9 45.2 20.2 . . . .
<3.67>
3.78 - 3.56 2.6 13.6 17.8 45.4 20.6 . . . .
<3.68>
3.56 - 3.38 2.0 12.5 16.6 47.5 21.4 . . . .
<3.74>
3.38 - 3.23 1.2 11.3 17.8 48.2 21.4 . . . .
<3.78>
3.23 - 3.11 1.4 11.7 18.6 47.1 21.1 . . . .
<3.76>
3.11 - 3.00 1.0 11.3 19.0 48.1 20.6 . . . .
<3.77>
- - - - - - ----- ----- ----- ----- ----- ----- ----- ----- ----- ->>>
* 30.0 - 3.00 2.1 14.5 18.5 45.3 19.6 0.0 0.0 0.0 0.0 100.
<3.66>
----------- ----- ----- ----- ----- ----- ----- ----- ----- ----- ====
------
Below specified lower-resolution limit :
inf. - 30.0 . 100.0 . . . . . . .
<2.00>
Beyond specified high-resolution limit :
3.00 - 2.99 . 30.3 20.5 41.8 7.4 . . . .
<3.27>
Multiplicity of centric measurements
Shell- 1* 2* 3* 4* 5-6* 7-8* 9-12* >13* total / poss.
C[%]
limits [A] ----- ----- ----- ----- ----- ----- ----- ----- ----- -----
----
30.0 - 6.46 93 354 32 2 0 0 0 0 481 566
85.0
6.46 - 5.13 37 251 28 0 0 0 0 0 316 334
94.6
5.13 - 4.48 39 209 16 0 0 0 0 0 264 281
94.0
4.48 - 4.07 24 193 17 0 0 0 0 0 234 249
94.0
4.07 - 3.78 25 169 21 0 0 0 0 0 215 223
96.4
3.78 - 3.56 34 161 18 0 0 0 0 0 213 220
96.8
3.56 - 3.38 25 157 17 0 0 0 0 0 199 204
97.5
3.38 - 3.23 26 145 21 0 0 0 0 0 192 192
100.0
3.23 - 3.11 26 138 23 0 0 0 0 0 187 187
100.0
3.11 - 3.00 27 129 19 0 0 0 0 0 175 175
100.0
- - - - - - ----- ----- ----- ----- ----- ----- ----- ----- ----- -----
----
* 30.0 - 3.00 356 1906 212 2 0 0 0 0 2476 2631
94.1
Multiplicity of acentric measurements for Bijvoet /-/ and /+/ separately :
Shell- 1* 2* 3* 4* 5-6* 7-8* 9-12* >13* total / poss.
C[%]
limits [A] ----- ----- ----- ----- ----- ----- ----- ----- ----- -----
----
30.0 - 6.46 1530 4572 790 0 0 0 0 0 6892 7534
91.5
6.46 - 5.13 1503 4925 1077 0 0 0 0 0 7505 7720
97.2
5.13 - 4.48 1786 4813 974 0 0 0 0 0 7573 7796
97.1
4.48 - 4.07 1811 4668 1066 0 0 0 0 0 7545 7754
97.3
4.07 - 3.78 1686 4685 1209 0 0 0 0 0 7580 7834
96.8
3.78 - 3.56 1756 4595 1308 0 0 0 0 0 7659 7882
97.2
3.56 - 3.38 1785 4558 1407 0 0 0 0 0 7750 7896
98.2
3.38 - 3.23 1784 4527 1425 0 0 0 0 0 7736 7812
99.0
3.23 - 3.11 1833 4549 1415 0 0 0 0 0 7797 7908
98.6
3.11 - 3.00 1819 4405 1420 0 0 0 0 0 7644 7826
97.7
- - - - - - ----- ----- ----- ----- ----- ----- ----- ----- ----- -----
----
* 30.0 - 3.00 17293 46297 12091 0 0 0 0 0 75681 77962
97.1
Anomalous R-value :
( sum |<I+>-<I->| / sum |<I+>+<I->| ) = 17.5 %
where <I>=sum(Ij)/N,
calculated from 37074 anomalous pairs (with 143188 measurements:
multiplicity 2.1 <-> 78993 measurements
for I+
multiplicity 1.7 <-> 64195 measurements
for I-
Weighted anomalous R-value :
( sum |<I+>-<I->| / sum |<I+>+<I->| ) = 18.4 %
where <I>=sum(wj*Ij) with sum(wj)=1,
calculated from 37074 anomalous pairs
Table of s-dependent anomalous, and centric, R-factors in equal-volume
shells :
R_ano. = sum { |<I+> - <I->| } / sum { |<I+> + <I->| }
R_cen. = linear R_merge for centric reflexions only.
centric
Resolution s Bijvoet-pairs <I> R_ano. measurements
R_cen.
-----[A]---- ------------- ------- --[%]-- | -------
--[%]--
30.0 - 6.46 0.000 - 0.077 3252 10168. 12.79 | 806
29.64
6.46 - 5.13 0.077 - 0.097 3673 2734. 15.19 | 564
20.88
5.13 - 4.48 0.097 - 0.112 3694 4719. 16.01 | 440
24.88
4.48 - 4.07 0.112 - 0.123 3682 4326. 17.18 | 418
23.54
4.07 - 3.78 0.123 - 0.132 3678 2602. 19.76 | 375
27.71
3.78 - 3.56 0.132 - 0.141 3724 1490. 22.87 | 337
29.09
3.56 - 3.38 0.141 - 0.148 3806 1032. 26.32 | 317
34.76
3.38 - 3.23 0.148 - 0.155 3830 728. 31.24 | 317
35.64
3.23 - 3.11 0.155 - 0.161 3844 470. 38.98 | 292
47.76
3.11 - 3.00 0.161 - 0.167 3779 358. 48.06 | 250
59.71
- - - - - - -------- ------- ------- | -------
--[%]--
* 30.0 - 3.00 total : 36962 2745. 17.45% | 4116
28.09%
-------- ------- ------- -------
Below specified lower-resolution limit :
inf. - 30.0 0.000 - 0.017 1 110. 19.20 |
0
Beyond specified high-resolution limit :
3.00 - 2.99 0.167 - 0.167 111 340. 44.46 |
0
Summary of neg. <I> : 179 centric reflexions
2886 /I-/
2594 /I+/
including 0 pairs with *both* mates <=0
Tables of s-dependent R-factors in equal-volume shells :
(Single measurements or negative <I> omitted from all sums.)
R_linear = sum { |I - <I>| } / sum {I}
R_square = SQRT( sum{|I - <I>|**2} / sum{I**2} )
Resolution s measurements I<0 <I> <I/s> R_squ.
R_lin.
-----[A]---- ------------- -------- ----- ------- ----- --[%]--
--[%]--
30.0 - 6.46 0.000 - 0.077 12293 119 10081. 5.2 27.28
18.23
6.46 - 5.13 0.077 - 0.097 13386 394 2490. 2.7 19.45
18.50
5.13 - 4.48 0.097 - 0.112 12787 359 4220. 3.0 21.40
18.89
4.48 - 4.07 0.112 - 0.123 12670 452 3638. 2.5 21.79
21.21
4.07 - 3.78 0.123 - 0.132 12819 799 2102. 1.6 23.85
26.60
3.78 - 3.56 0.132 - 0.141 12820 940 1335. 1.1 26.50
32.14
3.56 - 3.38 0.141 - 0.148 12270 1186 958. 0.9 30.64
37.29
3.38 - 3.23 0.148 - 0.155 12071 1438 661. 0.6 36.79
44.73
3.23 - 3.11 0.155 - 0.161 11613 1619 463. 0.5 43.91
53.68
3.11 - 3.00 0.161 - 0.167 10870 1708 376. 0.4 51.01
61.37
- - - - - - ------ ------ ------- ----- -------
-------
* 30.0 - 3.00 total : 123599 9014 2674. 1.9 26.11%
22.61%
------ ------
=======
4515 non-pos. <I> with 9771 measurements omitted from this table.
Table of <<I>/sigma(<I>)> for mean values on output file:
================
Resolution <I> /0/ /+/ /-/
sig<0
-----[A]---- ------------- ------------- ------------- -------------
-----
30.0 - 6.46 4121 7.7 481 4.5 3551 5.8 3341
5.7 0
6.46 - 5.13 4148 4.6 316 2.5 3797 3.5 3708
3.2 0
5.13 - 4.48 4143 5.0 264 2.6 3838 3.8 3735
3.5 0
4.48 - 4.07 4097 4.3 234 2.1 3835 3.2 3710
3.0 0
4.07 - 3.78 4117 3.0 215 1.7 3863 2.2 3717
2.1 0
3.78 - 3.56 4148 2.2 213 1.6 3915 1.6 3744
1.5 0
3.56 - 3.38 4143 1.6 199 1.3 3938 1.2 3812
1.1 0
3.38 - 3.23 4098 1.2 192 0.9 3896 0.8 3840
0.8 0
3.23 - 3.11 4140 0.8 187 0.5 3946 0.6 3851
0.6 0
3.11 - 3.00 4040 0.6 175 0.4 3853 0.4 3791
0.4 0
- - - - - - ------------- ------------- ------------- -------------
-----
* 30.0 - 3.00 41195 3.1 2476 2.2 38432 2.3 37249
2.1 0
------------- ------------- ------------- -------------
-----
Below specified lower-resolution limit :
inf. - 30.0 1 -1.0 0 ... 1 -0.2 1
-1.0 0
Beyond specified high-resolution limit :
3.00 - 2.99 122 0.6 10 0.6 112 0.4 111
0.4 0
Multiplicity-independent and sigma-weighted R-factors :
PCV = "pooled coefficient of variation"
R_rim = "redundancy-independent merging R-factor" = R_meas.
R_pim = "precision-indicating merging R-factor"
Rw_xxx = sigma-weighted R-factors, where :
<Iw> = sum{ w * I } with sum{ w } = 1
.. defined as:
PCV = sum{ SQRT[ sum{ |Ij - <Ihkl>|**2 }/(n-1) ] } / sum{ <I> }
h j h
R_rim = sum{ SQRT[n/(n-1)] * sum{ |I - <Ihkl>| } } / sum{ I }
R_pim = sum{ SQRT[1/(n-1)] * sum{ |I - <Ihkl>| } } / sum{ I } )
Rw_rim = sum{ SQRT[n/(n-1)] * sum{ w * |I - <Iw>| } } / sum{<Iw>}
Rw_pim = sum{ SQRT[1/(n-1)] * sum{ w * |I - <Iw>| } } / sum{<Iw>}
Rw_squ = SQRT[ sum{ w * |I - <Iw>|**2 } / sum{<Iw>**2} ]
Rw_lin = sum{ w * |I - <Iw>| } / sum{<Iw>}
Resolution /+//-/ PCV R_rim R_pim Rw_rim Rw_pim Rw_squ.
Rw_lin.
-----[A]---- -------- --[%]-- --[%]-- --[%]-- --[%]-- --[%]-- --[%]--
--[%]--
30.0 - 6.46 5734 25.53 24.98 16.99 13.73 9.41 11.97
9.96
6.46 - 5.13 6143 25.77 25.31 17.18 22.87 15.69 15.44
16.57
5.13 - 4.48 5903 26.43 25.94 17.69 21.78 14.98 15.39
15.75
4.48 - 4.07 5800 29.69 29.07 19.78 25.73 17.66 18.16
18.65
4.07 - 3.78 5810 36.85 36.38 24.69 32.42 22.21 20.15
23.54
3.78 - 3.56 5768 44.37 43.66 29.37 40.40 27.53 25.67
29.44
3.56 - 3.38 5475 51.15 50.32 33.56 46.70 31.61 30.79
34.22
3.38 - 3.23 5375 61.60 60.34 40.23 56.21 38.02 37.98
41.20
3.23 - 3.11 5175 73.50 72.31 48.10 66.85 45.19 46.53
49.03
3.11 - 3.00 4833 83.97 82.72 55.07 77.06 52.10 57.35
56.51
--------- ------- ------- ------- ------- ------- -------
-------
* total : 56016 31.39% 30.88% 20.91% 24.72% 16.90% 13.95%
17.97%
--
============================================================================
Bart Hazes (Associate Professor)
Dept. of Medical Microbiology & Immunology
University of Alberta
1-15 Medical Sciences Building
Edmonton, Alberta
Canada, T6G 2H7
phone: 1-780-492-0042
fax: 1-780-492-7521
============================================================================
|
