(* Units are pixels for real space quantities, or reciprocal pixels *) (* for reciprocal space quantities, unless otherwise stated. The units *) (* refer to the sampled image. The spatial frequencies for filters are *) (* multiplied by the sampling factor and thus refer to the unsampled, *) (* raw image. *) (* ====================================================================*) (* comments that start with AP are replaced with user defined values *) (* from within Appion. *) (* ====================================================================*) tiltseries { W = { 2478, 2844 } (* AP orig window *) O = 500.446827525 (* AP orig thickness *) S = 8 (* AP sampling *) N = W/S (* window size at sampling S *) T = O/S (* thickness at sampling S *) F = 0.515082955379 (* AP cos( highest tilt angle ) *) sampling: S binning: true (* AP enable/disable binning of raw images *) preprocessing: true (* AP enable or disable preprocessing of raw images *) select: "0-999999" (* AP select specific images in the tilt series *) exclude: "999999" (* AP exclude specific images from the tilt series *) preprocess { logging: false border: 100 clip: { 3.5, 3.5 } (* specified as a multiple of the standard deviation *) thr: { 0.0, 999999.0 } (* specified as density values *) grow: 0 mask { gradient: true iter: false filter: "median" kernel: { 5, 5 } clip: { 3.5, 3.5 } } } window { size: N area: 0.95 (* AP window area *) mask { apodization: { 10, 10 } width: { 284, 330 } (* If working on your own, consider using N - 2.5 * apodization *) } lowpass { diameter: { 0.499553571429, 0.499553571429 } (* AP lowpass diameter *) (* If working on your own, consider using { lp_diam_x, lp_diam_y } * S *) apodization: { 0.199821428571, 0.199821428571 } (* AP lowpass apodization *) (* If working on your own, consider using { lp_apod_x, lp_apod_y } * S *) } highpass { diameter: { 0.00645701096365, 0.00645701096365 } (* AP highpass diameter *) (* If working on your own, consider using { lp_diam_x, lp_diam_y } * S *) apodization: { 0.0129140219273, 0.0129140219273 } (* AP highpass apodization *) (* If working on your own, consider using { hp_apod_x, hp_apod_y } * S *) } } reference { body: T / F slab: true (* AP slab-like object *) select: "0-999999" (* AP select specific images in the tilt series *) exclude: "999999" (* AP exclude specific images from the tilt series *) } align { estimate: false maxcorrection: 999999.0 maxshift: 999999.0 translimit: 301.0 norotations: false include: "0-999999" (* AP select specific images in the tilt series *) exclude: "999999" (* AP exclude specific images from the tilt series *) mask { apodization: { 10, 10 } width: { 284, 330 } (* If working on your own, consider using N - 2.5 * apodization *) } correlation { mode: "mcf" (* AP corr mode *) size: { 160, 160 } } peaksearch { radius: { 300.0, 300.0 } cmdiameter: { 0.0, 0.0 } (* AP_optional_cmdiameter *) (* Note: { 0, 0 } is equivalent to turning cmdiameter off *) } } fit { orientation: true azimuth: true elevation: false rotation: true scale: false include: "0-999999" (* AP select specific images in the tilt series *) exclude: "999999" (* AP exclude specific images from the tilt series *) logging: true (* AP enable diagnostic terminal output *) loglevel: 2 (* AP increase verbosity of diagnostic output *) } map { size: { 479, 463, 125 } (* AP reconstruction map size *) body: T / F slab: true (* AP slab-like object *) sampling: 8 (* AP reconstruction map sampling *) select: "0-999999" (* AP select specific images in the tilt series reconstruction *) exclude: "999999" (* AP exclude specific images from the tilt series reconstruction *) lowpass { (* AP lowpass map *) diameter: { 0.499553571429, 0.499553571429 } (* If working on your own, consider using { lp_diam_x, lp_diam_y } * S *) } logging: false (* AP enable diagnostic terminal output *) } (* prefix: "" AP prefix for input and output files *) suffix: ".mrc" (* AP filetype extension for images *) pathlist: "/gpfs/appion/jbrasch/19feb06g/protomo_alignments/tiltseries0024_thick1400/raw" (* AP path to raw directory *) cachedir: "/gpfs/appion/jbrasch/19feb06g/protomo_alignments/tiltseries0024_thick1400/cache" (* AP directory where cache files are stored *) outdir: "/gpfs/appion/jbrasch/19feb06g/protomo_alignments/tiltseries0024_thick1400/out" (* AP directory where other output files are stored *) logging: true (* AP enable diagnostic terminal output *) }