Dear ccp4 members
I have question about how to interpret polarrfn log. I wish to know if my
crystal display NCS. I am not sure how to interpret the file. I see it have two
peak, one is origin and the other is not that high to me. I have attach copy of
the file. If someone could assist me to understand the file it would be
appreciated.
best
Careina
#CCP4I VERSION CCP4Interface 2.0.5
#CCP4I SCRIPT LOG polarrfn
#CCP4I DATE 02 Jun 2011 08:39:42
#CCP4I USER sylvia
#CCP4I PROJECT H74A
#CCP4I JOB_ID 13
#CCP4I SCRATCH /tmp/sylvia
#CCP4I HOSTNAME occam.gh.wits.ac.za
#CCP4I PID 3351
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### CCP4 6.1: POLARRFN version 6.1 : 15/01/07##
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User: unknown Run date: 2/ 6/2011 Run time: 08:39:42
Please reference: Collaborative Computational Project, Number 4. 1994.
"The CCP4 Suite: Programs for Protein Crystallography". Acta Cryst. D50,
760-763.
as well as any specific reference in the program write-up.
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Data line--- title srf
Data line--- SELF
Data line--- CRYSTAL FILE 1
Data line--- LABIN FILE 1 F=F SIGF=SIGF
Data line--- PLOT
Data line--- FIND 10.0 10
Data line--- NOPRINT
Data line--- END
Using 1 files
OPENED INPUT MTZ FILE
Logical Name: HKLIN Filename:
/home/users/sylvia/Protein_Crystallography/CLIC1/H74A/10m_bioc7_clic_H74A_0f_truncate1.mtz
* Title:
import
* Base dataset:
0 HKL_base
HKL_base
HKL_base
* Number of Datasets = 1
* Dataset ID, project/crystal/dataset names, cell dimensions, wavelength:
1 H74A
H74A
H74A
82.1987 41.5416 66.7048 90.0000 90.0000 90.0000
1.54178
* Number of Columns = 8
* Number of Reflections = 20319
* Missing value set to NaN in input mtz file
* HISTORY for current MTZ file :
From FREERFLAG 15/11/2010 08:08:22 with fraction 0.050
data from CAD on 15/11/10
* Column Labels :
H K L FreeR_flag F SIGF I SIGI
* Column Types :
H H H I F Q J Q
* Associated datasets :
0 0 0 0 1 1 1 1
* Cell Dimensions : (obsolete - refer to dataset cell dimensions above)
82.1987 41.5416 66.7048 90.0000 90.0000 90.0000
* Resolution Range :
0.00037 0.29382 ( 51.796 - 1.845 A )
* Sort Order :
1 2 3 0 0
* Space group = 'P212121' (number 19)
Data line--- LABIN F=F SIGF=SIGF
Spacegroup information obtained from library file:
Logical Name: SYMINFO Filename:
/home/protein-software/CCP4/ccp4-6.1.2/lib/data/syminfo.lib
Polar angle rotation function: Self-rotation function
=======================================================
Title: srf
Integration radius = 20.00A Resolution limits 51.80 2.00
Radius for averaging (smoothing) 1.400
Crystal 1: orthogonalisation code (NCODE) = 1 x y z axes along a,c*xa,c*
Space group 19 (P212121), 4 symmetry operations
Temperature factor = 0.000
Fmin = 0. Fmax = 1.0000E+20
Cell dimensions: 82.20 41.54 66.70 90.00 90.00 90.00
Ranges & steps in phi = 0.00 180.00 2.00
Ranges & steps in omega = 0.00 180.00 2.00
Ranges & steps in kappa = 0.00 180.00 2.00
Sections will be searched for a maximum of 10 peaks above a threshold of
10.000
LMAX = 54 NUMBER OF SPHERICAL HARMONIC COEFFICIENTS = 4244
NMAX(L) 19 18 17 16 15 14 13 12 11 11 10 9 8 8 7 6 6 5
4 4
3 3 2 2 1 1 1
UNFORMATTED SCRATCH file opened on unit 8
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Logical name: COEFFS1, Filename: /tmp/sylvia/polarrfn_CF1.03352
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Crystal number : 1
Basis set (orthogonalisation matrix) : 82.19870 0.00005 0.00008
0.00000 41.54160 0.00008
0.00000 0.00000 66.70480
Symmetry operation 1: 1 0 0
0 1 0
0 0 1
Symmetry operation 2: 1 0 0
0 -1 0
0 0 -1
Symmetry operation 3: -1 0 0
0 1 0
0 0 -1
Symmetry operation 4: -1 0 0
0 -1 0
0 0 1
Crystal 1 15973 reflections read 0 reflections too
large
Numbers of reflections in ranges of sin**2 theta / lambda**2
1 575
2 964
3 1220
4 1423
5 1619
6 1749
7 1929
8 2052
9 2164
10 2278
Printed norms should be exactly 1:
Omega L M Norm (min) L M Norm (max)
0.00 0 0 1.000000E+00 0 0 1.000000E+00
2.00 36 1 1.000000E+00 54 13 1.000000E+00
4.00 54 1 1.000000E+00 52 35 1.000000E+00
6.00 54 52 1.000000E+00 52 0 1.000000E+00
8.00 36 19 1.000000E+00 54 0 1.000000E+00
10.00 32 23 1.000000E+00 52 0 1.000000E+00
12.00 32 25 1.000000E+00 52 10 1.000000E+00
14.00 54 1 1.000000E+00 52 35 1.000000E+00
16.00 32 1 1.000000E+00 52 0 1.000000E+00
18.00 34 1 1.000000E+00 54 5 1.000000E+00
20.00 36 3 1.000000E+00 52 35 1.000000E+00
22.00 54 1 1.000000E+00 52 35 1.000000E+00
24.00 38 1 1.000000E+00 52 35 1.000000E+00
26.00 38 1 1.000000E+00 52 35 1.000000E+00
28.00 36 3 1.000000E+00 52 11 1.000000E+00
30.00 48 0 1.000000E+00 52 42 1.000000E+00
32.00 44 4 1.000000E+00 52 42 1.000000E+00
34.00 34 21 1.000000E+00 52 0 1.000000E+00
36.00 36 3 1.000000E+00 52 35 1.000000E+00
38.00 36 3 1.000000E+00 52 10 1.000000E+00
40.00 36 3 1.000000E+00 52 10 1.000000E+00
42.00 36 3 1.000000E+00 52 11 1.000000E+00
44.00 46 9 1.000000E+00 52 42 1.000000E+00
46.00 46 7 1.000000E+00 52 42 1.000000E+00
48.00 36 3 1.000000E+00 54 9 1.000000E+00
50.00 36 3 1.000000E+00 52 11 1.000000E+00
52.00 36 3 1.000000E+00 52 11 1.000000E+00
54.00 36 3 1.000000E+00 52 11 1.000000E+00
56.00 36 3 1.000000E+00 52 23 1.000000E+00
58.00 36 36 1.000000E+00 52 11 1.000000E+00
60.00 36 3 1.000000E+00 52 21 1.000000E+00
62.00 36 3 1.000000E+00 52 50 1.000000E+00
64.00 36 3 1.000000E+00 52 11 1.000000E+00
66.00 36 3 1.000000E+00 52 23 1.000000E+00
68.00 36 3 1.000000E+00 52 52 1.000000E+00
70.00 36 3 1.000000E+00 52 11 1.000000E+00
72.00 36 3 1.000000E+00 52 10 1.000000E+00
74.00 36 21 1.000000E+00 52 23 1.000000E+00
76.00 36 3 1.000000E+00 52 11 1.000000E+00
78.00 36 3 1.000000E+00 52 11 1.000000E+00
80.00 36 3 1.000000E+00 52 11 1.000000E+00
82.00 36 3 1.000000E+00 52 11 1.000000E+00
84.00 36 21 1.000000E+00 52 11 1.000000E+00
86.00 36 3 1.000000E+00 52 21 1.000000E+00
88.00 36 3 1.000000E+00 52 11 1.000000E+00
90.00 10 0 1.000000E+00 52 11 1.000000E+00
92.00 36 3 1.000000E+00 52 11 1.000000E+00
94.00 36 3 1.000000E+00 52 23 1.000000E+00
96.00 36 3 1.000000E+00 52 11 1.000000E+00
98.00 36 3 1.000000E+00 52 23 1.000000E+00
100.00 36 3 1.000000E+00 52 11 1.000000E+00
102.00 36 3 1.000000E+00 52 11 1.000000E+00
104.00 36 21 1.000000E+00 52 21 1.000000E+00
106.00 36 3 1.000000E+00 52 11 1.000000E+00
108.00 36 3 1.000000E+00 52 52 1.000000E+00
110.00 36 3 1.000000E+00 52 23 1.000000E+00
112.00 36 3 1.000000E+00 52 52 1.000000E+00
114.00 36 3 1.000000E+00 52 23 1.000000E+00
116.00 36 3 1.000000E+00 52 11 1.000000E+00
118.00 36 3 1.000000E+00 52 50 1.000000E+00
120.00 36 3 1.000000E+00 52 51 1.000000E+00
122.00 34 34 1.000000E+00 52 11 1.000000E+00
124.00 36 3 1.000000E+00 52 21 1.000000E+00
126.00 44 11 1.000000E+00 52 51 1.000000E+00
128.00 36 3 1.000000E+00 52 11 1.000000E+00
130.00 36 3 1.000000E+00 52 52 1.000000E+00
132.00 36 3 1.000000E+00 52 11 1.000000E+00
134.00 36 3 1.000000E+00 52 52 1.000000E+00
136.00 36 3 1.000000E+00 52 11 1.000000E+00
138.00 46 9 1.000000E+00 52 43 1.000000E+00
140.00 36 3 1.000000E+00 54 9 1.000000E+00
142.00 36 3 1.000000E+00 52 11 1.000000E+00
144.00 34 23 1.000000E+00 54 9 1.000000E+00
146.00 36 3 1.000000E+00 52 11 1.000000E+00
148.00 22 1 1.000000E+00 54 9 1.000000E+00
150.00 46 9 1.000000E+00 52 43 1.000000E+00
152.00 34 23 1.000000E+00 54 9 1.000000E+00
154.00 32 25 1.000000E+00 52 11 1.000000E+00
156.00 38 1 1.000000E+00 54 9 1.000000E+00
158.00 22 17 1.000000E+00 52 11 1.000000E+00
160.00 34 23 1.000000E+00 54 9 1.000000E+00
162.00 32 23 1.000000E+00 52 23 1.000000E+00
164.00 32 1 1.000000E+00 54 5 1.000000E+00
166.00 54 1 1.000000E+00 52 23 1.000000E+00
168.00 54 1 1.000000E+00 52 23 1.000000E+00
170.00 48 0 1.000000E+00 52 35 1.000000E+00
172.00 48 0 1.000000E+00 52 35 1.000000E+00
174.00 46 3 1.000000E+00 52 35 1.000000E+00
176.00 38 1 1.000000E+00 54 2 1.000000E+00
178.00 34 3 1.000000E+00 54 2 1.000000E+00
180.00 0 0 1.000000E+00 0 0 1.000000E+00
Maximum R = 0.4621E+05
END PLOT: Picture number 1
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END PLOT: Picture number 91
Unpermuted symmetry operations for crystal 1:
Symmetry matrix 1 1.00000 0.00000 0.00000
0.00000
0.00000 1.00000 0.00000
0.00000
0.00000 0.00000 1.00000
0.00000
Symmetry matrix 2 1.00000 0.00000 0.00000
0.50000
0.00000 -1.00000 0.00000
0.50000
0.00000 0.00000 -1.00000
0.00000
Symmetry matrix 3 -1.00000 0.00000 0.00000
0.00000
0.00000 1.00000 0.00000
0.50000
0.00000 0.00000 -1.00000
0.50000
Symmetry matrix 4 -1.00000 0.00000 0.00000
0.50000
0.00000 -1.00000 0.00000
0.00000
0.00000 0.00000 1.00000
0.50000
Positions of 10 peaks above 10.
Eulerian angles Polar angles
Alpha Beta Gamma Peak Omega Phi Kappa
Direction cosines
Symmetry: 1 2
Peak 1
Origin peak 100.0 0.0 0.0 0.0
Peak 2
1 1 0.0 0.0 180.0 100.0 0.0 0.0 3.1
0.0000 0.0000 1.0000
1 2 0.0 180.0 0.0 100.0 90.0 90.0 3.1
0.0000 1.0000 0.0000
1 3 0.0 180.0 180.0 100.0 90.0 0.0 3.1
1.0000 0.0000 0.0000
Origin peak 100.0 0.0 0.0 180.0
Peak 3
1 1 0.0 0.0 180.0 100.0 0.0 0.0 3.1
0.0000 0.0000 1.0000
1 2 0.0 180.0 0.0 100.0 90.0 90.0 3.1
0.0000 1.0000 0.0000
1 3 0.0 180.0 180.0 100.0 90.0 0.0 3.1
1.0000 0.0000 0.0000
Origin peak 100.0 180.0 0.0 180.0
Peak 4
1 1 0.0 180.0 0.0 100.0 90.0 90.0 3.1
0.0000 1.0000 0.0000
1 2 0.0 0.0 180.0 100.0 0.0 0.0 3.1
0.0000 0.0000 1.0000
Origin peak 100.0 90.0 90.0 180.0
Peak 5
1 1 0.0 180.0 180.0 100.0 90.0 0.0 3.1
1.0000 0.0000 0.0000
Origin peak 100.0 90.0 180.0 180.0
Peak 6
1 1 0.0 180.0 180.0 100.0 90.0 0.0 3.1
1.0000 0.0000 0.0000
Origin peak 100.0 90.0 0.0 180.0
Peak 7
1 1 0.0 0.0 285.3 29.5 180.0 180.0 74.7
0.0000 0.0000 -1.0000
1 2 0.0 180.0 254.7 29.5 90.0 142.7 180.0
-0.7952 0.6063 0.0000
1 3 0.0 180.0 74.7 29.5 90.0 232.7 180.0
-0.6063 -0.7952 0.0000
1 4 0.0 0.0 105.3 29.5 0.0 61.4 105.3
0.0000 0.0000 1.0000
2 1 0.0 180.0 105.3 29.5 90.0 37.3 180.0
0.7952 0.6063 0.0000
2 2 0.0 0.0 74.7 29.5 0.0 39.5 74.7
0.0000 0.0000 1.0000
2 3 0.0 0.0 254.7 29.5 180.0 184.4 105.3
0.0000 0.0000 -1.0000
2 4 0.0 180.0 285.3 29.5 90.0 127.3 180.0
-0.6063 0.7952 0.0000
3 1 0.0 180.0 285.3 29.5 90.0 307.3 180.0
0.6063 -0.7952 0.0000
3 2 0.0 0.0 254.7 29.5 180.0 170.7 105.3
0.0000 0.0000 -1.0000
3 3 0.0 0.0 74.7 29.5 0.0 124.5 74.7
0.0000 0.0000 1.0000
3 4 0.0 180.0 105.3 29.5 90.0 37.3 180.0
0.7952 0.6063 0.0000
4 1 0.0 0.0 105.3 29.5 0.0 136.6 105.3
0.0000 0.0000 1.0000
4 2 0.0 180.0 74.7 29.5 90.0 232.7 180.0
-0.6063 -0.7952 0.0000
4 3 0.0 180.0 254.7 29.5 90.0 322.7 180.0
0.7952 -0.6063 0.0000
4 4 0.0 0.0 285.3 29.5 180.0 188.0 74.7
0.0000 0.0000 -1.0000
Peak 8
1 1 0.0 0.0 74.7 29.5 0.0 0.0 74.7
0.0000 0.0000 1.0000
1 2 0.0 180.0 105.3 29.5 90.0 37.3 180.0
0.7952 0.6063 0.0000
1 3 0.0 180.0 285.3 29.5 90.0 127.3 180.0
-0.6063 0.7952 0.0000
1 4 0.0 0.0 254.7 29.5 180.0 209.6 105.3
0.0000 0.0000 -1.0000
2 1 0.0 180.0 254.7 29.5 90.0 142.7 180.0
-0.7952 0.6063 0.0000
2 2 0.0 0.0 285.3 29.5 180.0 142.6 74.7
0.0000 0.0000 -1.0000
2 3 0.0 0.0 105.3 29.5 0.0 97.7 105.3
0.0000 0.0000 1.0000
2 4 0.0 180.0 74.7 29.5 90.0 232.7 180.0
-0.6063 -0.7952 0.0000
3 1 0.0 180.0 74.7 29.5 90.0 232.7 180.0
-0.6063 -0.7952 0.0000
3 2 0.0 0.0 105.3 29.5 0.0 97.6 105.3
0.0000 0.0000 1.0000
3 3 0.0 0.0 285.3 29.5 180.0 232.6 74.7
0.0000 0.0000 -1.0000
3 4 0.0 180.0 254.7 29.5 90.0 142.7 180.0
-0.7952 0.6063 0.0000
4 1 0.0 0.0 254.7 29.5 180.0 135.1 105.3
0.0000 0.0000 -1.0000
4 2 0.0 180.0 285.3 29.5 90.0 307.3 180.0
0.6063 -0.7952 0.0000
4 3 0.0 180.0 105.3 29.5 90.0 37.3 180.0
0.7952 0.6063 0.0000
4 4 0.0 0.0 74.7 29.5 0.0 82.4 74.7
0.0000 0.0000 1.0000
Peak 9
1 1 0.0 0.0 254.6 29.5 180.0 180.0 105.4
0.0000 0.0000 -1.0000
1 2 0.0 180.0 285.4 29.5 90.0 127.3 180.0
-0.6059 0.7956 0.0000
1 3 0.0 180.0 105.4 29.5 90.0 217.3 180.0
-0.7956 -0.6059 0.0000
1 4 0.0 0.0 74.6 29.5 0.0 32.9 74.6
0.0000 0.0000 1.0000
2 1 0.0 180.0 74.6 29.5 90.0 232.7 180.0
-0.6059 -0.7956 0.0000
2 2 0.0 0.0 105.4 29.5 0.0 54.9 105.4
0.0000 0.0000 1.0000
2 3 0.0 0.0 285.4 29.5 180.0 347.2 74.6
0.0000 0.0000 -1.0000
2 4 0.0 180.0 254.6 29.5 90.0 142.7 180.0
-0.7956 0.6059 0.0000
3 1 0.0 180.0 254.6 29.5 90.0 322.7 180.0
0.7956 -0.6059 0.0000
3 2 0.0 0.0 285.4 29.5 180.0 184.9 74.6
0.0000 0.0000 -1.0000
3 3 0.0 0.0 105.4 29.5 0.0 141.0 105.4
0.0000 0.0000 1.0000
3 4 0.0 180.0 74.6 29.5 90.0 232.7 180.0
-0.6059 -0.7956 0.0000
4 1 0.0 0.0 74.6 29.5 0.0 137.9 74.6
0.0000 0.0000 1.0000
4 2 0.0 180.0 105.4 29.5 90.0 37.3 180.0
0.7956 0.6059 0.0000
4 3 0.0 180.0 285.4 29.5 90.0 127.3 180.0
-0.6059 0.7956 0.0000
4 4 0.0 0.0 254.6 29.5 180.0 172.0 105.4
0.0000 0.0000 -1.0000
Peak 10
1 1 0.0 0.0 105.4 29.5 0.0 180.0 105.4
0.0000 0.0000 1.0000
1 2 0.0 180.0 74.6 29.5 90.0 52.7 180.0
0.6059 0.7956 0.0000
1 3 0.0 180.0 254.6 29.5 90.0 142.7 180.0
-0.7956 0.6059 0.0000
1 4 0.0 0.0 285.4 29.5 180.0 240.4 74.6
0.0000 0.0000 -1.0000
2 1 0.0 180.0 285.4 29.5 90.0 307.3 180.0
0.6059 -0.7956 0.0000
2 2 0.0 0.0 254.6 29.5 180.0 127.3 105.4
0.0000 0.0000 -1.0000
2 3 0.0 0.0 74.6 29.5 0.0 82.3 74.6
0.0000 0.0000 1.0000
2 4 0.0 180.0 105.4 29.5 90.0 37.3 180.0
0.7956 0.6059 0.0000
3 1 0.0 180.0 105.4 29.5 90.0 37.3 180.0
0.7956 0.6059 0.0000
3 2 0.0 0.0 74.6 29.5 0.0 262.3 74.6
0.0000 0.0000 1.0000
3 3 0.0 0.0 254.6 29.5 180.0 217.3 105.4
0.0000 0.0000 -1.0000
3 4 0.0 180.0 285.4 29.5 90.0 127.3 180.0
-0.6059 0.7956 0.0000
4 1 0.0 0.0 285.4 29.5 180.0 135.0 74.6
0.0000 0.0000 -1.0000
4 2 0.0 180.0 254.6 29.5 90.0 322.7 180.0
0.7956 -0.6059 0.0000
4 3 0.0 180.0 74.6 29.5 90.0 232.7 180.0
-0.6059 -0.7956 0.0000
4 4 0.0 0.0 105.4 29.5 0.0 97.7 105.4
0.0000 0.0000 1.0000
The rotation given by the angles of a peak rotates coordinates in the
orthogonal frame
of crystal 2 to the orthogonal frame of crystal 1.
Beware of axis permutations introduced by NCODE = 2, 3 or 4
Rotation matrices are defined as follows:
( l**2+(m**2+n**2)cos k lm(1-cos k)-nsin k nl(1-cos k)+msin k )
( lm(1-cos k)+nsin k m**2+(l**2+n**2)cos k mn(1-cos k)-lsin k )
Polar angles
( nl(1-cos k)-msin k mn(1-cos k)+lsin k n*2+(l**2+m**2)cos k )
where l m n are the direction cosines of the axis about which the rotation
k = kappa takes place.
( l ) ( sin omega cos phi )
( m ) = ( sin omega sin phi )
( n ) ( cos omega )
( cosa cosb cosg - sina sing -cosa cosb sing - sina cosg cosa sinb )
( sina cosb cosg + cosa sing -sina cosb sing + cosa cosg sina sinb )
Eulerian angles Alpha, Beta, Gamma
( -sinb cosg sinb sing cosb )
Weighted mean of map -0.003
Weighted rms 7.297
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POLARRFN: Normal Termination from POLARRFN
Times: User: 33.6s System: 0.1s Elapsed: 0:34
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#CCP4I TERMINATION STATUS 1
#CCP4I TERMINATION TIME 02 Jun 2011 08:40:16
#CCP4I MESSAGE Task completed successfully
