function [ a , b ] = t r a n s f o r m ( proj , raw )
% Sabrina Fiedler
% MATLAB 2017b / 2018a
5 p r o j = p r o j ( : ) ; raw = raw ( : ) ;
M = s i z e( proj , 1 ) ;
tmp = M sum( p r o j . raw ) ≠ sum( p r o j ) . sum( raw ) ;
10 a = tmp / (M sum( p r o j .^2 ) ≠ sum( p r o j ) . ^2 ) ; b = 1/M (sum( raw ) ≠ a sum( p r o j ) ) ;
end
Listing B.4: Least square transformation
Main
f i l e n a m e 1 = ’ e i n s t e i n R i b o 2 _ a 1 b 0 e i n s t e i n R i b o 2 _ a 1 b 0 . mat ’; f i l e n a m e 2 = ’ e i n s t e i n R i b o 1 _ a 1 b 0 e i n s t e i n R i b o 1 _ a 1 b 0 . mat ’; f i l e n a m e = s t r c a t (’ s i n g l e ’ , f i l e n a m e 1 ) ;
5 load( filename1 , ’ f r e q s ’) ; load( filename1 , ’ t ot al N ’) ;
%% all
10 N = 2 t ot al N ;
SNR_total = cat (1 ,load( filename1 ,’SNR ’) ,load( filename2 ,’SNR ’) ) ; SSNR_total = cat (1 ,load( filename1 ,’SSNR ’) ,load( filename2 , ’SSNR ’) ) ;
15 SNR = cat (1 , SNR_total (2) . SNR, SNR_total (1) .SNR) ; SSNR = cat (1 , SSNR_total (2) . SSNR , SSNR_total (1) . SSNR) ;
FSC = double (ReadMRC2D(’ f s c . mrc ’ ,1 ,1) ) ;
% per Image
Listing B.5: main for the ribosome data
% Sabrina Fiedler
end
40
FRC = 1/ t o t al N sum(FRC ’ , 2 ) ; summedS = 1/ t o tal N sum(S ’ , 2 ) ;
45 f i l e n a m e = ’ SNRdividedByNoise_90percent_2 ’; csvwrite( s t r c a t ( filename , ’SSNR . csv ’) ,SSNR) ;
csvwrite( s t r c a t ( filename , ’SNR. csv ’) ,SNR) ; save( s t r c a t ( filename , titleName ,’ . mat ’) ) ;
50
% twoAxis(freqs(1,2:end),FRC(2:end,1),’FRC’,FSC(2:end,1),’FSC’,summedS (2:end,1),’SSNR’,strcat(filename,’Snr.fig’),titleName);
Listing B.6: main
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CC cross-correlation. 32, 54, 95
cryo-EM electron cryo-microscopy. iii, iv, xi, xii, 2, 4–10, 12–14, 17, 19–27, 29, 30, 33, 38, 39, 41, 44, 48, 49, 51–57, 60, 63–66, 70–74, 78, 80–88, 91–96, 98–103, 105, 106, 111 cs-thm central-slice theorem. xi, 27, 38, 49, 50, 56, 67, 70
CTF Contrast Transfer Function. iv, xi, xii, 10–12, 26, 40, 46, 47, 51, 55–59, 78, 92–94, 105
DFT Discrete Fourier Transform. 34 DPR Differential Phase Residual. 52 DQE detective quantum efficiency. 17 EM electron microscopy. 3–5
EMDB Electron Microscopy Data Bank. 6, 7, 106 FFT Fast Fourier Transform. xi, 22, 27, 34–37
FRC of projections Fourier Ring Correlation of projections. iv, xii, xv, 71–73, 76–83, 88–91, 94, 96, 102, 105, 116
FSC Fourier Shell Correlation. iii, iv, xi, xii, 21–26, 30, 52–60, 63, 65–68, 71–73, 76, 77, 79, 80, 91, 93–99, 101, 102, 105
FSC of reconstruction Fourier Shell Correlation of reconstruction. xii, 73, 76–83, 88 FT Fourier Transform. 33, 34
IFFT Inverse Fast Fourier Transform. 34, 50 IFT Inverse Fourier Transform. 34
NCC normalized cross-correlation. 22, 32, 50, 101
NMR spectroscopy Nuclear Magnetic Resonance Spectroscopy. 3–5, 106 PCA Principal Component Analysis. 48
PSF Point Spread Function. 10, 44
QSNR Quality Signal-to-Noise-Ratio. xii, xv, 69–72, 85, 88–90, 94, 96, 115, 116
QSSNR Quality-Spectral Signal-to-Noise-Ratio. iv, xv, 70–73, 76–83, 85, 89–91, 96, 102, 112, 116
RCSB PDB Protein Data Bank. xi, 3–5, 58, 61, 62
RELION REgularized LIkelihood OptiminzatioN. xi, 8, 29, 51, 52, 56, 57, 59, 65, 66, 79, 82, 83, 85, 87, 91, 92, 97, 98, 100, 105
SEM Scanning Electron Microscope. 4
SNR Signal-to-Noise-Ratio. iii, iv, xiii, 7, 10, 14, 15, 17, 20, 21, 24–26, 45–49, 53–55, 61, 73, 80, 84, 88, 91, 92, 95, 96, 98, 100–102, 105
SPA single particle analysis. iii, iv, 4, 6, 8, 13, 17, 20, 29, 45, 48, 52, 56, 88, 95, 98, 111 SSNR Spectral Signal-to-Noise-Ratio. iv, 30, 52–54, 68, 71, 101, 102, 105
STEM Scanning Transmission Electron Microscope. 4
TEM Transmission Electron Microscope. iii, iv, xi, 4, 6–12, 15–17, 19–21, 38–46, 55, 56, 61, 62, 68, 69, 91, 92, 131
WPO weak-phase-object. iv, 9, 26, 94
XRC X-Ray Diffraction Crystallography. 3–5, 106
N The number of images in the data set. 46 ú convolution of two functions f úg. 37
IÂrk the k-th detected single particle projection image. 68, 70, 84, 86, 87, 102, 103
IÂsk thek-th re-projection image with respect to the reconstruction. 68, 84, 86, 87, 102, 103 C complex space. 30
N complex space. 30 R real space. 30
µm Micormeter is a metrical unit. 11, 93 eV The energy of an electron. 41
keV The accelerating voltage of the TEM. 39, 41 mm Millimeter is a metrical unit. 41
nm Nanometer is a metrical unit. 3, 41 pm Picometer is a metrical unit.. 3, 41
Å Angstroem is a metrical unit with Å equal to 10≠10m. 2, 7, 11, 18, 21, 23–25, 38, 56, 57, 59–61, 63, 65, 66, 74, 76–83, 88, 89
2D Two-dimensional object with Kn◊n. xi, 8, 10, 12, 22, 30–32, 34, 35, 37, 38, 41, 46–51, 67, 68, 74, 97, 113
3D three-dimensional map. iii, iv, 6, 8, 10, 12, 13, 15, 17–19, 21–24, 26, 30, 32, 38, 45–52, 56–59, 62, 64–67, 78, 82, 85, 93, 95, 96, 98, 103, 107
MDa Mega Dalton. 6