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Merging in 2dx_merge in 2D
This processing merges several images into one dataset. This here describes the merging of several non-tilted images into a two-dimensional dataset.
origtiltd
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takes several APH/${imagename}.fou.cor.aph
generates APH/merge.aph, which now has for each spot potentially many entries
Filename: APH/merge.aph
1: Header
2: H K Z* AMP PHS NO IQ WEIGHT BACK CTF
AMP is the raw measured value, not yet changed
PHS is CTF phase flipped, and has also the PhaseOrigin applied to it
WEIGHT is .... ToDo
Example:
1001
1 0 -0.0000 70.8670 -88.1100 65551 -6 0.078805 47.8734 -0.083
1 0 0.0000 112.300 -21.6200 6543 6 0.192624 74.5000 -0.093
1 0 0.0000 25.0594 -131.430 65551 8 0.027867 49.3105 -0.088
1 0 0.0000 31.3698 -46.4300 665202 8 0.055313 44.8141 -0.094
1 0 -0.0000 29.1893 -120.570 655302 -8 0.045419 35.9687 -0.096
...
2 0 -0.0000 120.801 -160.000 6557 4 0.192729 48.7613 -0.165
2 0 -0.0000 156.540 169.480 665202 -2 0.276022 34.6150 -0.154
2 0 -0.0000 202.253 170.080 655201 -3 0.375352 51.5399 -0.167
2 0 0.0000 9.95763 167.980 655502 8 0.013483 37.5852 -0.138
2 0 -0.0000 102.017 167.300 655502 4 0.138136 42.3687 -0.122
...
2 0 0.0013 411.287 -178.300 7032 1 0.440457 50.2215 -0.383
2 0 0.0013 313.198 -178.300 8032 2 0.307053 40.1020 -0.385
2 0 0.0016 298.834 -161.900 5685 2 0.360523 61.4043 -0.198
2 0 0.0019 296.552 176.500 6666 2 0.338671 57.6485 -0.250
2 0 0.0024 330.403 -177.000 8005 1 0.263018 33.6716 -0.509
avramphs:
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uses zminmax = -0.025...0.025, to make sure only non-tilted data participate.
takes APH/merge.aph
generates APH/avrg2D.hkl
Filename: APH/avrg2D.hkl
1: merging number
2: H K L AMP PHS FOM
AMP is an average of several spots, and the values are now amplitude-CTF corrected (without inverting the sign).
PHS is an average of several spots, which are already CTF and phaseorigin corrected
FOM is calculated as.....ToDo
Example:
1001
1 0 0 196.833 -64.0629 96.9797
1 1 0 1018.19 -6.10076 99.9556
1 2 0 162.905 -177.142 98.7745
1 3 0 262.806 -179.891 99.5678
1 4 0 123.772 -152.694 97.1893
...
2 0 0 453.627 -177.303 99.8751
2 1 0 109.832 4.30570 94.4169
2 2 0 1278.94 177.975 99.9585
2 3 0 288.222 179.579 99.7178
2 4 0 382.900 -2.25470 99.9126
centric2.exe:
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takes APH/avrg2D.hkl
generates APH/centric2D.hkl
Filename: APH/centric2D.hkl
1: Header
2: H K L AMP PHS FOM
Example:
1001
1 2 0 162.905 180.000 98.7745
1 3 0 262.806 180.000 99.5678
1 4 0 123.772 180.000 88.8569
1 5 0 272.380 180.000 99.8588
1 6 0 287.654 180.000 99.9085
...
2 0 0 453.627 180.000 99.8751
2 1 0 109.832 0.00000 94.4169
2 2 0 1278.94 180.000 99.9376
2 3 0 288.222 180.000 99.7178
2 4 0 382.900 0.00000 99.9126
2dx_hklsym.exe:
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takes APH/centric2D.hkl
generates APH/sym_noheader2D.hkl
Filename: APH/sym_noheader2D.hkl
1: Header
2: H K L AMP PHS FOM
Example:
0 2 0 453.627 -180.000 99.8751
0 -2 0 453.627 180.000 99.8751
0 -2 0 453.627 -180.000 99.8751
0 2 0 453.627 180.000 99.8751
-2 0 0 453.627 -180.000 99.8751
2 0 0 453.627 180.000 99.8751
2 0 0 453.627 -180.000 99.8751
-2 0 0 453.627 180.000 99.8751
0 3 0 350.611 0.00000 99.5364
0 -3 0 350.611 -0.00000 99.5364
0 -3 0 350.611 0.00000 99.5364
0 3 0 350.611 -0.00000 99.5364
sort:
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takes APH/sym_noheader2D.hkl
generates APH/sym_sort2D.hkl
2dx_hklclean.exe:
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takes APH/sym_sort2D.hkl
generates APH/sym2D.hkl
Filename: APH/sym2D.hkl
1: Header
2: H K L AMP PHS FOM
Example:
0 2 0 453.627 180.000 99.8800
0 3 0 350.611 0.00000 99.5400
0 4 0 523.815 0.00000 99.9000
0 5 0 839.137 180.000 99.9500
0 6 0 673.367 180.000 99.9500
...
2 0 0 453.627 180.000 99.8800
2 1 0 109.832 0.00000 94.4200
2 2 0 1278.94 180.000 99.9400
2 3 0 288.222 180.000 99.7200
2 4 0 382.900 0.00000 99.9100
f2mtz.exe:
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takes APH/sym2D.hkl
generates merge2D.mtz
Filename: merge2D.mtz
SYMMETRY ${CCP4_SYM}
LABOUT H K L F PHI FOM
CTYPOUT H H H F P W
