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Merging in 2dx_merge in 3D
This processing merges several images into one dataset. This here describes the merging of several tilted images into a three-dimensional dataset.
latlinprescal.exe:
-
uses zminmax limitation (e.g. zminmax = -0.2....0.2)
uses IQMAX limitation (e.g. IQ<=4)
takes APH/merge.aph
Filename: APH/merge.aph
2: H K Z* AMP PHS NO IQ WEIGHT BACK CTF
AMP is original, not CTF corrected.
PHS is CTF corrected (potentially phase flipped by adding 180.0, and also PhaseOrigin corrected.)
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
generates SCRATCH/latlines.dat
Filename: SCRATCH/latlines.dat
1: H K Z* AMP PHI SIGAMP SIGPHI IQ
AMP is an average of several spots, and the values are now CTF amplitude corrected, but the sign is not changed.
PHS is CTF corrected (potentially phase flipped by adding 180.0, and also PhaseOrigin corrected.)
SIGAMP is the sigma of the amplitude. It is BACK/abs(CTF)
SIGPHI is the sigma of the phase. It is 1/SQRT(IQWeight*WeightFactor)
Example:
1 0 0.00060 104.16600 -52.049999 46.001900 84.006340 4
1 0 0.00080 268.98999 -12.300000 80.155701 34.477715 3
1 0 0.00220 184.12601 -139.35001 87.379898 56.066078 4
1 0 0.00270 202.74899 -53.500000 51.419800 43.694344 3
1 0 0.00290 335.90900 -39.549999 127.63800 42.084263 4
...
2 0 -0.00000 120.80100 -160.00000 48.761299 63.911808 4
2 0 -0.00000 156.53999 169.48000 34.615002 20.773575 2
2 0 -0.00000 202.25301 170.08000 51.539902 32.058155 3
2 0 -0.00000 102.01700 167.30000 42.368698 75.492043 4
2 0 0.00000 166.73900 -163.96001 34.383202 20.128237 2
...
2 0 0.00130 411.28699 -178.30000 50.221500 12.333118 1
2 0 0.00130 313.19800 -178.30000 40.102001 19.695927 2
2 0 0.00160 298.83401 -161.89999 61.404301 18.176765 2
2 0 0.00190 296.55200 176.50000 57.648499 18.754007 2
2 0 0.00240 330.40302 -177.00000 33.671600 15.959963 1
2 0 0.00350 464.72900 -176.30000 55.043598 10.858499 1
2 0 0.00440 397.06299 159.89999 57.502399 14.851025 2
latlined.exe:
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takes SCRATCH/latlines.dat
generates SCRATCH/latfitteds.dat
Filename: SCRATCH/latfitteds.dat
1: H K evenly-spaced-Z* Fcalc Phicalc SigmaF SigmaPhi FOM
(FOM = cos(SigmaPhi))
Example:
1 0 0.00000 247.55566 0.0000000 18.924459 21.598083 0.92978877
1 0 0.00500 209.19904 6.0731225 23.460869 100.000000 0.0000000
1 0 0.01000 117.95479 17.182913 77.827194 100.000000 0.0000000
1 1 0.00000 506.22305 0.0000000 20.299940 23.113247 0.91973072
1 1 0.00500 552.17487 -4.4475732 32.424282 100.000000 0.0000000
1 1 0.01000 646.05676 -4.7668672 39.198265 100.000000 0.0000000
...
2 0 0.00000 242.33742 180.00000 13.209599 3.6789784 0.99793923
2 0 0.00500 268.57681 -146.76134 14.605533 20.451212 0.93697006
2 0 0.01000 269.84033 -125.68211 16.254116 37.249146 0.79601103
2 0 0.01500 187.71519 -96.291374 29.352510 47.953720 0.66973066
2 0 0.02000 186.94331 -25.610069 33.024536 35.831753 0.81073952
2 0 0.02500 341.22220 5.1924558 34.590252 33.411781 0.83473468
2 1 0.00000 60.028835 0.0000000 13.363790 86.333664 0.63945934E-01
2 1 0.00500 97.333725 3.7004271 21.510071 100.000000 0.0000000
2 1 0.01000 169.23180 4.2294579 15.836013 100.000000 0.0000000
prepmklcf.exe
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takes SCRATCH/latfitteds.dat
generates APH/latfitted_nosym.hkl
Filename: APH/latfitted_nosym.hkl
1: H K L AMP PHS FOM
FOM=100.0*COS(SIGPR) ; SIGPR=SIGP*ReductionFactorForPhaseAccuracy
Example:
1 0 0 247.55566 0.0000000 91.525581
1 1 0 506.22305 0.0000000 90.315102
1 2 0 170.77887 180.00000 94.623932
1 2 1 185.55049 -170.90527 79.694740
1 3 0 146.51767 180.00000 97.948296
...
2 0 0 242.33742 180.00000 99.750671
2 0 1 268.57681 -146.76134 92.390381
2 0 2 269.84033 -125.68211 75.500603
2 0 3 187.71519 -96.291374 60.530575
2 0 4 186.94331 -25.610069 77.256760
2 0 5 341.22220 5.1924558 80.122246
2 2 0 752.02271 180.00000 96.488884
2 3 0 100.37424 180.00000 99.041061
and generates APH/latfittedref_nosym.hkl
Filename: APH/latfittedref_nosym.hkl
1: H K L AMP PHS FOM SIGA
FOM=100.0*COS(SIGPR) ; SIGPR=SIGP*ReductionFactorForPhaseAccuracy
SIGA=SigmaF from input file
Example:
1 0 0 247.55566 0.0000000 91.525581 18.924459
1 1 0 506.22305 0.0000000 90.315102 20.299940
1 2 0 170.77887 180.00000 94.623932 23.181156
1 2 1 185.55049 -170.90527 79.694740 25.114998
1 3 0 146.51767 180.00000 97.948296 18.022064
...
2 0 0 242.33742 180.00000 99.750671 13.209599
2 0 1 268.57681 -146.76134 92.390381 14.605533
2 0 2 269.84033 -125.68211 75.500603 16.254116
2 0 3 187.71519 -96.291374 60.530575 29.352510
2 0 4 186.94331 -25.610069 77.256760 33.024536
2 0 5 341.22220 5.1924558 80.122246 34.590252
2 2 0 752.02271 180.00000 96.488884 35.606602
2 3 0 100.37424 180.00000 99.041061 29.780148
2 3 1 238.15096 132.77484 92.741394 33.503052
2 3 2 383.73682 137.60635 94.809868 36.883396
2dx_hklsym.exe: for volume
-
takes APH/latfitted_nosym.hkl
generates APH/latfitted_sym_nosort.hkl
Filename: APH/latfitted_sym_nosort.hkl
1: H K L AMP PHASE FOM
Example:
0 1 0 247.55566 0.0000000 91.525581
0 -1 0 247.55566 -0.0000000 91.525581
0 -1 0 247.55566 0.0000000 91.525581
0 1 0 247.55566 -0.0000000 91.525581
-1 0 0 247.55566 0.0000000 91.525581
1 0 0 247.55566 -0.0000000 91.525581
1 0 0 247.55566 0.0000000 91.525581
-1 0 0 247.55566 -0.0000000 91.525581
0 2 0 242.33742 -179.99997 99.750671
0 -2 0 242.33742 179.99997 99.750671
0 -2 0 242.33742 -179.99997 99.750671
0 2 0 242.33742 179.99997 99.750671
-2 0 0 242.33742 -179.99997 99.750671
2 0 0 242.33742 179.99997 99.750671
2 0 0 242.33742 -179.99997 99.750671
-2 0 0 242.33742 179.99997 99.750671
0 2 1 268.57681 -146.76135 92.390381
0 -2 -1 268.57681 146.76135 92.390381
0 -2 1 268.57681 -146.76135 92.390381
0 2 -1 268.57681 146.76135 92.390381
sort: for volume
-
takes APH/latfitted_sym_nosort.hkl
generates APH/latfitted_sym_sort.hkl
Filename: APH/latfitted_sym_sort.hkl
1: H K L AMP PHASE FOM
Example:
0 1 0 247.55566 0.0000000 91.525581
0 1 0 247.55566 0.0000000 91.525581
0 1 0 247.55566 -0.0000000 91.525581
0 1 0 247.55566 -0.0000000 91.525581
0 2 0 242.33742 179.99997 99.750671
0 2 0 242.33742 179.99997 99.750671
0 2 0 242.33742 -179.99997 99.750671
0 2 0 242.33742 -179.99997 99.750671
0 2 1 268.57681 -146.76135 92.390381
0 2 1 268.57681 -146.76135 92.390381
0 2 2 269.84033 -125.68211 75.500603
0 2 2 269.84033 -125.68211 75.500603
2dx_hklsym.exe: for reference
-
takes APH/latfittedref_nosym.hkl
generates APH/latfittedref_sym_nosort.hkl
Filename: APH/latfittedref_sym_nosort.hkl
1: H K L AMP PHASE FOM SIGA
Example:
0 1 0 247.55566 0.0000000 91.525581 18.924459
0 -1 0 247.55566 -0.0000000 91.525581 18.924459
0 -1 0 247.55566 0.0000000 91.525581 18.924459
0 1 0 247.55566 -0.0000000 91.525581 18.924459
-1 0 0 247.55566 0.0000000 91.525581 18.924459
1 0 0 247.55566 -0.0000000 91.525581 18.924459
1 0 0 247.55566 0.0000000 91.525581 18.924459
-1 0 0 247.55566 -0.0000000 91.525581 18.924459
0 2 0 242.33742 -179.99997 99.750671 13.209599
0 -2 0 242.33742 179.99997 99.750671 13.209599
0 -2 0 242.33742 -179.99997 99.750671 13.209599
0 2 0 242.33742 179.99997 99.750671 13.209599
-2 0 0 242.33742 -179.99997 99.750671 13.209599
2 0 0 242.33742 179.99997 99.750671 13.209599
2 0 0 242.33742 -179.99997 99.750671 13.209599
-2 0 0 242.33742 179.99997 99.750671 13.209599
sort: for reference
-
takes APH/latfittedref_sym_nosort.hkl
generates APH/latfittedref_sym_sort.hkl
Filename: APH/latfittedref_sym_sort.hkl
1: H K L AMP PHASE FOM SIGA
Example:
0 1 0 247.55566 0.0000000 91.525581 18.924459
0 1 0 247.55566 0.0000000 91.525581 18.924459
0 1 0 247.55566 -0.0000000 91.525581 18.924459
0 1 0 247.55566 -0.0000000 91.525581 18.924459
0 2 0 242.33742 179.99997 99.750671 13.209599
0 2 0 242.33742 179.99997 99.750671 13.209599
0 2 0 242.33742 -179.99997 99.750671 13.209599
0 2 0 242.33742 -179.99997 99.750671 13.209599
0 2 1 268.57681 -146.76135 92.390381 14.605533
0 2 1 268.57681 -146.76135 92.390381 14.605533
0 2 2 269.84033 -125.68211 75.500603 16.254116
0 2 2 269.84033 -125.68211 75.500603 16.254116
0 2 3 187.71519 -96.291382 60.530575 29.352510
2dx_hlkclean: for volume
-
takes APH/latfitted_sym_sort.hkl
generates APH/latfitted.hkl
Filename: APH/latfitted.hkl
1: H K L AMP PHASE FOM
Example:
0 1 0 247.55566 0.0000000 91.525581
0 2 0 242.33742 179.99997 99.750671
0 2 1 268.57681 -146.76135 92.390381
0 2 2 269.84033 -125.68211 75.500603
0 2 3 187.71519 -96.291382 60.530575
0 2 4 186.94331 -25.610071 77.256760
0 2 5 341.22220 5.1924558 80.122246
2dx_hlkclean: for reference
-
takes APH/latfittedref_sym_sort.hkl
generates APH/latfittedref.hkl
Filename: APH/latfittedref.hkl
1: H K L AMP PHASE FOM SIGA
Example:
0 1 0 247.55566 0.0000000 91.525581 18.924459
0 2 0 242.33742 179.99997 99.750671 13.209599
0 2 1 268.57681 -146.76135 92.390381 14.605533
0 2 2 269.84033 -125.68211 75.500603 16.254116
0 2 3 187.71519 -96.291382 60.530575 29.352510
0 2 4 186.94331 -25.610071 77.256760 33.024536
0 2 5 341.22220 5.1924558 80.122246 34.590252
0 2 -1 268.57681 146.76135 92.390381 14.605533
0 2 -2 269.84033 125.68211 75.500603 16.254116
f2mtz: for volume
-
takes APH/latfitted.hkl
generates merge3D.mtz
Filename: merge3D.mtz
SYMMETRY ${CCP4_SYM}
LABOUT H K L F PHI FOM
CTYPOUT H H H F P W
f2mtz: for reference
-
takes APH/latfittedref.hkl
generates merge3Dref.mtz
Filename: merge3Dref.mtz
SYMMETRY ${CCP4_SYM}
LABOUT H K L F PHI FOM SIGA
CTYPOUT H H H F P W W