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Processing in 2dx_image of ONE image
This processing deals only with one single image and is therefore two-dimensional processing.
UNBEND II: mmboxa.exe:
- takes FFTIR/cor${imagename}.fft.mrc
generates APH/${imagename}.fou.nolimit.aph
Filename: APH/${imagename}.fou.nolimit.aph
1: Header
2: H K AMP PHS IQ BCK CTF
Example:
655201 gf06552, Unbend2, Mon Jun 16 00:33:23 CEST 2008
0 1 0.0 60.9 9 72.2 0.0
0 2 165.8 330.8 3 49.3 0.0
0 3 17.1 52.3 8 39.3 0.0
0 4 151.8 123.1 2 36.5 0.0
0 5 411.8 127.5 2 50.9 0.0
CORRECT CTF: ctfapply.exe:
-
takes ${imagename}.fou.nolimit.aph
generates ${imagename}.fou.ctf.nolimit.aph
Filename: ${imagename}.fou.ctf.nolimit.aph
1: Header
2: H K AMP PHS IQ BCK CTF
AMP is not changed
PHS is already CTF-applied, possibly +180.
CTF lists the contrast. Only phase (sign) was already applied.
Example:
655201 gf06552, Thu Jul 3 22:49:19 PDT 2008
0 1 0.0 240.9 9 72.2 -0.096
0 2 165.8 150.8 3 49.3 -0.172
0 3 17.1 232.3 8 39.3 -0.295
0 4 151.8 303.1 2 36.5 -0.459
0 5 411.8 307.5 2 50.9 -0.648
GENERATE MAP: origtiltd
-
takes APH/${imagename}.fou.cor.aph
generates APH/${prefix}${imagename}.cor.origtiltd.aph
Filename: APH/${prefix}${imagename}.cor.origtiltd.aph
1: Header
2: H K Z* AMP PHS NO IQ WEIGHT BACK CTF
AMP is not changed
PHS now has also the PhaseOrigin applied to it
WEIGHT is calculated as .... ToDo
Example:
655201
0 2 0.0000 165.8 167.2 655201 3 0.66720 49.3 -0.172
0 3 0.0000 17.1 76.8 655201 8 0.51724 39.3 -0.295
0 4 0.0000 151.8 -24.2 655201 2 0.65309 36.5 -0.459
0 5 0.0000 411.8 168.4 655201 2 0.91529 50.9 -0.648
avramphs:
-
takes APH/${prefix}${imagename}.cor.origtiltd.aph
generates ${prefix}avrg.hkl
Filename: ${prefix}avrg.hkl
1: Header
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, and already is CTF corrected (possibly +180)
FOM is calculated as.....ToDo
Example:
655201
0 2 0 331.6 167.2 93.898
0 3 0 34.2 76.8 12.381
0 4 0 303.6 -24.2 98.200
0 5 0 635.5 168.4 98.200
centric2.exe:
-
takes ${prefix}avrg.hkl
generates ${prefix}centric.hkl
Filename: ${prefix}centric.hkl
1: Header
2: H K L AMP PHS FOM
Example:
655201
0 2 0 331.6 167.2 93.898
0 3 0 34.2 76.8 12.381
0 4 0 303.6 -24.2 98.200
0 5 0 635.5 168.4 98.200
f2mtz.exe:
-
takes ${prefix}centric.hkl
generates ${prefix}${imagename}.mtz
Filename: ${prefix}${imagename}.mtz
LABOUT H K L F PHI FOM
CTYPOUT H H H F P W