THIS FILE IS JUST THE LOG FOR ONE CHUNK AND WAS COPIED BY PROCESSCHUNKS FROM tilt-001.log *** Entries to program tilt *** InputProjections = MTEg5series6D.ali OutputFile = MTEg5series6D_full.rec ActionIfGPUFails = 2,2 AdjustOrigin = 1 BoundaryInfoFile = tilt-bound.info EXCLUDELIST2 = 1 FULLIMAGE = 4096 3072 IMAGEBINNED = 1 LOG = 0.0 MODE = 1 OFFSET = 0.0 PERPENDICULAR = 1 RADIAL = 0.35 0.05 SCALE = 0.0 250.0 SHIFT = 0.0 0.0 SLICE = 0 383 SUBSETSTART = 0 0 THICKNESS = 300 TILTFILE = MTEg5series6D.tlt TOTALSLICES = 0 3071 UseGPU = 0 XAXISTILT = -2.07 XTILTFILE = MTEg5series6D.xtilt *** End of entries *** RO image file on unit 1 : MTEg5series6D.ali Size= 1499137 K Number of columns, rows, sections ..... 4096 3072 61 Map mode .............................. 1 (16-bit integer) Start cols, rows, sects, grid x,y,z ... 0 0 0 4096 3072 61 Pixel spacing (Angstroms).............. 5.300 5.300 5.300 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 ....................... 22.000 Maximum density ....................... 971.00 Mean density .......................... 377.60 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: Boulder 3DEM TF20 16-Oct-13 16:00:27 Tilt axis angle = -3.3, binning = 1 spot = 6 camera = 1 CCDERASER: Bad points replaced with interpolated values 21-Oct-13 14:34:36 NEWSTACK: Images copied, transformed 5-Nov-13 14:18:16 ctfPhaseFlip: CTF correction with phase flipping only 05-Nov-13 14:18:53 CCDERASER: Bad points replaced with interpolated values 5-Nov-13 14:27:00 Radial weighting function parameters IRMAX = 1433 IWIDE = 204 Output map densities incremented by 0.00 and then multiplied by 250.00 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/NOBACKUP/mast/MTEg5_101013/MTEg5series6D/MTEg5series6D.tlt FORMATTED ro file opened: /home/NOBACKUP/mast/MTEg5_101013/MTEg5series6D/MTEg5series6D.xtilt Constant alpha tilt of 0.0 to be applied based on angles from file Global alpha tilt of -2.1 will be applied ------------------------------------------------------------------------------ Rows 1 to 384, (at intervals of 1) of the projection planes will be reconstructed. Thickness of reconstructed slice is 300 pixels. Full aligned stack will be assumed to be 4096 by 3072 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 3072 Tilt angles were entered from a tilt file OLD image file on unit 2 : MTEg5series6D_full.rec Size= 1 K Number of columns, rows, sections ..... 4096 300 3072 Map mode .............................. 1 (16-bit integer) Start cols, rows, sects, grid x,y,z ... 0 0 0 4096 300 3072 Pixel spacing (Angstroms).............. 5.300 5.300 5.300 Cell angles ........................... 90.000 90.000 90.000 Fast, medium, slow axes ............... X Y Z Origin on x,y,z ....................... 0.000 795.0 0.000 Minimum density ....................... 22.000 Maximum density ....................... 971.00 Mean density .......................... 377.60 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: Boulder 3DEM TF20 16-Oct-13 16:00:27 Tilt axis angle = -3.3, binning = 1 spot = 6 camera = 1 CCDERASER: Bad points replaced with interpolated values 21-Oct-13 14:34:36 NEWSTACK: Images copied, transformed 5-Nov-13 14:18:16 ctfPhaseFlip: CTF correction with phase flipping only 05-Nov-13 14:18:53 CCDERASER: Bad points replaced with interpolated values 5-Nov-13 14:27:00 TILT: Tomographic reconstruction 5-Nov-13 14:31:21 Projection angles: -58.95 -56.95 -54.95 -52.95 -50.94 -48.94 -46.93 -44.93 -42.90 -40.88 -38.86 -36.83 -34.81 -32.79 -30.76 -28.74 -26.72 -24.70 -22.69 -20.68 -18.66 -16.65 -14.64 -12.63 -10.65 -8.66 -6.68 -4.69 -2.71 -0.73 1.23 3.19 5.15 7.11 9.07 11.03 12.99 15.00 17.02 19.03 21.04 23.05 25.07 27.06 29.06 31.05 33.05 35.05 37.03 39.00 40.98 42.96 44.94 46.94 48.94 50.93 52.93 54.92 56.91 58.90 ------------------------------------------------------------------------------ Allocated 86 MB for stack array Allocated 8 MB for arrays (including 1 input planes) on the GPU Using GPU for backprojection STACK LOADING ------------- Total stack size 22668577 Radial weighting 249600 function Output slice 1245184 15 Untilted slices 18677760 10 Transposed projections 2496000 NEW image file on unit 7 : MTEg5series6D_full-001.rbound Min, max, mean, # pixels= -8102.753 5071.722 127.0225 471859200. To scale output to bytes (10-245), use SCALE to add 34.653 and scale by 4.45938 To scale output to -15000 to 15000, use SCALE to add 6.062 and scale by 569.28265 Reconstruction of 384 slices complete. ------------------------------------------------------------------------------ SUCCESSFULLY COMPLETED CHUNK DONE