THIS FILE IS JUST THE LOG FOR ONE CHUNK AND WAS COPIED BY PROCESSCHUNKS FROM tilt-001.log *** Entries to program tilt *** InputProjections = WTI042413_1series4.ali OutputFile = WTI042413_1series4_full.rec ActionIfGPUFails = 2,2 AdjustOrigin = 1 BoundaryInfoFile = tilt-bound.info FULLIMAGE = 1852 1856 IMAGEBINNED = 1 MODE = 1 OFFSET = 0.0 PERPENDICULAR = 1 RADIAL = 0.35 0.05 SCALE = 0.0 0.1 SHIFT = 0.0 0.0 SLICE = 0 265 SUBSETSTART = 0 0 THICKNESS = 266 TILTFILE = WTI042413_1series4.tlt TOTALSLICES = 0 1855 UseGPU = 0 XAXISTILT = 1.65 XTILTFILE = WTI042413_1series4.xtilt *** End of entries *** RO image file on unit 1 : WTI042413_1series4.ali Size= 409524 K Number of columns, rows, sections ..... 1852 1856 61 Map mode .............................. 1 (16-bit integer) Start cols, rows, sects, grid x,y,z ... 0 0 0 1852 1856 61 Pixel spacing (Angstroms).............. 6.740 6.740 6.740 Cell angles ........................... 90.000 90.000 90.000 Fast, medium, slow axes ............... X Y Z Origin on x,y,z ....................... 0.000 0.000 0.000 Minimum density ....................... -250.00 Maximum density ....................... 886.00 Mean density .......................... 223.66 tilt angles (original,current) ........ 0.0 0.0 0.0 0.0 0.0 0.0 Space group,# extra bytes,idtype,lens . 0 0 0 0 6 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, undistorted 28-May-13 11:02:55 ctfPhaseFlip: CTF correction with phase flipping only 28-May-13 11:04:03 CCDERASER: Bad points replaced with interpolated values 28-May-13 13:09:31 Radial weighting function parameters IRMAX = 648 IWIDE = 92 Output map densities incremented by 0.00 and then multiplied by 0.10 Output map is sectioned perpendicular to the tilt axis Data mode of output file is 1 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 ------------------------------------------------------------------------------ Rows 1 to 266, (at intervals of 1) of the projection planes will be reconstructed. Thickness of reconstructed slice is 266 pixels. Full aligned stack will be assumed to be 1852 by 1856 pixels Aligned stack will be assumed to be a subset starting at 0 0 Computed slices are part of a total volume from slice 1 to 1856 Tilt angles were entered from a tilt file OLD image file on unit 2 : WTI042413_1series4_full.rec Size= 1 K Number of columns, rows, sections ..... 1852 266 1856 Map mode .............................. 1 (16-bit integer) Start cols, rows, sects, grid x,y,z ... 0 0 0 1852 266 1856 Pixel spacing (Angstroms).............. 6.740 6.740 6.740 Cell angles ........................... 90.000 90.000 90.000 Fast, medium, slow axes ............... X Y Z Origin on x,y,z ....................... 0.000 896.4 0.000 Minimum density ....................... -250.00 Maximum density ....................... 886.00 Mean density .......................... 223.66 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 7 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, undistorted 28-May-13 11:02:55 ctfPhaseFlip: CTF correction with phase flipping only 28-May-13 11:04:03 CCDERASER: Bad points replaced with interpolated values 28-May-13 13:09:31 TILT: Tomographic reconstruction 28-May-13 13:09:58 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 76 MB for stack array Allocated 3 MB for arrays (including 1 input planes) on the GPU Using GPU for backprojection STACK LOADING ------------- Total stack size 20000000 Radial weighting 116266 function Output slice 500040 12 Untilted slices 6000480 115 Transposed projections 13370590 NEW image file on unit 7 : WTI042413_1series4_full-001.rbound Min, max, mean, # pixels= -1247.180 1197.478 5.371078 131040112. To scale output to bytes (10-245), use SCALE to add 13512.079 and scale by 0.00961 To scale output to -15000 to 15000, use SCALE to add 248.508 and scale by 1.22717 Reconstruction of 266 slices complete. ------------------------------------------------------------------------------ SUCCESSFULLY COMPLETED CHUNK DONE