THIS FILE IS JUST THE LOG FOR ONE CHUNK AND WAS COPIED BY PROCESSCHUNKS FROM tilt_3dfind-001.log *** Entries to program tilt *** InputProjections = WTI042413_1series4_3dfind.ali OutputFile = WTI042413_1series4_3dfind.rec ActionIfGPUFails = 2,2 AdjustOrigin = 1 BoundaryInfoFile = tilt_3dfind-bound.info FULLIMAGE = 1852 1856 IMAGEBINNED = 3 LOG = 0.0 MODE = 1 OFFSET = 0.0 PERPENDICULAR = 1 RADIAL = 0.35 0.05 SCALE = 0.0 700.0 SHIFT = 0.0 9.1 SLICE = 0 153 SUBSETSTART = -1 -2 THICKNESS = 350 TILTFILE = WTI042413_1series4.tlt TOTALSLICES = 0 1857 XAXISTILT = 1.65 XTILTFILE = WTI042413_1series4.xtilt *** End of entries *** RO image file on unit 1 : WTI042413_1series4_3dfind.ali Size= 45651 K Number of columns, rows, sections ..... 618 620 61 Map mode .............................. 1 (16-bit integer) Start cols, rows, sects, grid x,y,z ... 0 0 0 618 620 61 Pixel spacing (Angstroms).............. 20.22 20.22 6.740 Cell angles ........................... 90.000 90.000 90.000 Fast, medium, slow axes ............... X Y Z Origin on x,y,z ....................... 6.740 13.48 0.000 Minimum density ....................... -32.245 Maximum density ....................... 734.46 Mean density .......................... 223.79 tilt angles (original,current) ........ 0.0 0.0 0.0 0.0 0.0 0.0 Space group,# extra bytes,idtype,lens . 0 854 0 0 4 Titles : SerialEM: Digitized on Janelia Krios 26-Apr-13 14:20:21 Tilt axis angle = 168.0, binning = 2 spot = 7 camera = 3 CCDERASER: Bad points replaced with interpolated values 26-Apr-13 17:17:47 NEWSTACK: Images copied, transformed 28-May-13 13:06:38 Radial weighting function parameters IRMAX = 216 IWIDE = 30 Output map densities incremented by 0.00 and then multiplied by 700.00 Output map is sectioned perpendicular to the tilt axis Data mode of output file is 1 Taking logarithm of input data plus 0.000 FORMATTED ro file opened: /home/cschwart/JaneliaFarms/WTI042413_1/series4/WTI042413_1series4.tlt FORMATTED ro file opened: /home/cschwart/JaneliaFarms/WTI042413_1/series4/WTI042413_1series4.xtilt Constant alpha tilt of 0.0 to be applied based on angles from file Global alpha tilt of 1.6 will be applied Dimensions and coordinates will be scaled down by a factor of 3 ------------------------------------------------------------------------------ Rows 1 to 52, (at intervals of 1) of the projection planes will be reconstructed. Thickness of reconstructed slice is 116 pixels. Full aligned stack will be assumed to be 618 by 619 pixels Aligned stack will be assumed to be a subset starting at 0 0 Output slice shifted up 3.0 and to right 0.0 pixels Computed slices are part of a total volume from slice 1 to 620 Tilt angles were entered from a tilt file OLD image file on unit 2 : WTI042413_1series4_3dfind.rec Size= 1 K Number of columns, rows, sections ..... 618 116 620 Map mode .............................. 1 (16-bit integer) Start cols, rows, sects, grid x,y,z ... 0 0 0 618 116 620 Pixel spacing (Angstroms).............. 20.22 20.22 20.22 Cell angles ........................... 90.000 90.000 90.000 Fast, medium, slow axes ............... X Y Z Origin on x,y,z ....................... 6.740 1234. 13.48 Minimum density ....................... -32.245 Maximum density ....................... 734.46 Mean density .......................... 223.79 tilt angles (original,current) ........ 0.0 0.0 0.0 90.0 0.0 0.0 Space group,# extra bytes,idtype,lens . 0 0 0 0 5 Titles : SerialEM: Digitized on Janelia Krios 26-Apr-13 14:20:21 Tilt axis angle = 168.0, binning = 2 spot = 7 camera = 3 CCDERASER: Bad points replaced with interpolated values 26-Apr-13 17:17:47 NEWSTACK: Images copied, transformed 28-May-13 13:06:38 TILT: Tomographic reconstruction 28-May-13 13:06:56 Projection angles: -58.94 -56.94 -54.92 -52.91 -50.92 -48.92 -46.93 -44.92 -42.91 -40.90 -38.89 -36.89 -34.90 -32.91 -30.92 -28.93 -26.94 -24.94 -22.93 -20.93 -18.93 -16.93 -14.93 -12.93 -10.92 -8.92 -6.92 -4.91 -3.02 -1.12 0.78 2.68 4.58 6.48 8.52 10.56 12.60 14.64 16.68 18.72 20.72 22.72 24.73 26.73 28.73 30.77 32.80 34.84 36.87 38.90 40.94 42.97 45.00 47.03 49.06 51.03 53.00 54.96 57.01 59.06 61.11 ------------------------------------------------------------------------------ Allocated 21 MB for stack array STACK LOADING ------------- Total stack size 5467131 Radial weighting 41114 function Output slice 74160 8 Untilted slices 593280 55 Transposed projections 4673570 Stretching buffer 84974 NEW image file on unit 7 : WTI042413_1series4_3dfind-001.rbound Min, max, mean, # pixels= -11512.83 9047.442 335.7011 3727776. To scale output to bytes (10-245), use SCALE to add 17.697 and scale by 8.00087 To scale output to -15000 to 15000, use SCALE to add 1.761 and scale by 1021.38721 Reconstruction of 52 slices complete. ------------------------------------------------------------------------------ SUCCESSFULLY COMPLETED CHUNK DONE