************ Version 7.0.0 (beta test) for Image plate and CCD data 14th June 2006 *********** A.G.W. Leslie, MRC Laboratory Of Molecular Biology, HILLS ROAD, CAMBRIDGE CB2 2QH, UK E-mail andrew@mrc-lmb.cam.ac.uk New auto-indexing using DPS due to Ingo Steller Robert Bolotovsky and Michael Rossmann (1998) J. Appl. Cryst. 30, 1036-1040 Original auto-indexing using REFIX due to Wolfgang Kabsch (Kabsch,W. (1993), J.Appl.Cryst. 24,795-800.) X-windows interface using xdl_view due to John Campbell (Daresbury Laboratory, UK.) (Campbell,J.W. (1995) J. Appl. Cryst. 28, 236-242. ===> newmat autoindex.mat ===> directory /mntdirect/_scisoft/users/svensson/WorkSpace-develop/TestCase ===> template ref-trypsin_1_###.img ===> beam 105.4 105.15 ===> BEST ON ===> prerefine on ****** Keyword NOT RECOGNISED ***** ===> autoindex dps refine image 1 thresh 20.000000 Using DPS code for background indexing Pre-refining solutions better than penalty of 200 prior to choosing a DPS solution ===> autoindex dps refine image 2 thresh 20.000000 Using DPS code for background indexing Pre-refining solutions better than penalty of 200 prior to choosing a DPS solution ===> mosaic estimate ===> go From information in the image file, the detector has been recognized as: ADSC If this is incorrect you must supply a DETECTOR keyword Crystal to detector distance of 116.02mm taken from image header Wavelength of 0.93400A taken from image header Pixel size of 0.1024mm taken from image header. Start and end phi values for image 0 from image header are 0.00 and 1.00 degrees. Oscillation axis set as PHI from image header ***** WARNING ***** ***** WARNING ***** ***** WARNING ***** ***** WARNING ***** Input beam coordinates 105.40mm 105.15mm DO NOT agree with those calculated from the image header ( 105.04mm 105.15mm) Autoindexing using 2 images Image numbers: 1 2 image FILENAME: /mntdirect/_scisoft/users/svensson/WorkSpace-develop/TestCase/ref-trypsin_1_001.img Determining average spot size for spots in centre of image. ========================================================== Determining best threshold for spot finding. Default parameters may be reset with SPOTS keyword. Minimum radius 10.4mm, maximum radius 41.90mm, minimum number of spots 10 Background strip overlaps gap between detector tiles, so YOFFSET changed to 5.2mm Number of spots excluded from possible ice rings: 42 Threshold set to 5.0 Number of spots excluded from possible ice rings: 57 Threshold set to 5.0 Based on a median spot size of 5 by 5 pixels in X and Y, the measurement box parameters have been set to 17 17 10 5 5 The overall size of the box has been fixed. To prevent this use keywords PROFILE NOFIXBOX. ***** WARNING ***** Lattice type not specified, so assumed primitive Based on a median spot size of 5 by 5 pixels in X and Y, the spot separation parameters (in X and Y) have been set to 0.71 0.71mm. Closest possible spot separation is 0.00mm. Determining best threshold for spot finding. Default parameters may be reset with SPOTS keyword. Minimum radius 19.1mm, maximum radius 41.90mm, minimum number of spots 10 Number of spots excluded from possible ice rings: 83 Threshold set to 5.0 Number of spots excluded from possible ice rings: 83 Threshold set to 5.0 Finding spots on image 1 (Midpoint of phi 0.500 degrees) Calculating radial background..... The background is radial along the X (slow) direction The average of 51 pixels, excluding outliers, is used The scan is offset by 5.8mm from the image centre in Y to avoid any backstop shadow Radial Background calculation complete RADIUS 19.1 19.6 20.0 20.4 20.8 21.2 21.6 22.0 22.4 22.8 23.2 23.7 BACKG 461 471 478 500 506 514 535 544 564 593 598 624 SIGMA 10 10 10 11 11 11 11 11 11 12 12 12 NREJ 28 32 35 26 27 24 29 31 31 27 35 33 RADIUS 24.1 24.5 24.9 25.3 25.7 26.1 26.5 26.9 27.3 27.8 28.2 28.6 BACKG 655 677 706 727 734 791 809 861 875 897 919 960 SIGMA 12 13 13 13 13 14 14 14 14 14 15 15 NREJ 31 35 32 31 38 32 34 25 27 30 34 28 RADIUS 29.0 29.4 29.8 30.2 30.6 31.0 31.4 31.8 32.3 32.7 33.1 33.5 BACKG 989 999 1018 1022 1041 1036 1057 1047 1029 1040 1024 1003 SIGMA 15 15 15 15 16 16 16 16 16 16 16 15 NREJ 25 25 18 24 21 29 14 25 30 15 16 20 RADIUS 33.9 34.3 34.7 35.1 35.5 35.9 36.4 36.8 37.2 37.6 38.0 38.4 BACKG 971 923 891 880 822 808 743 718 695 673 646 618 SIGMA 15 15 14 14 14 14 13 13 13 12 12 12 NREJ 30 37 34 23 37 34 41 37 34 30 28 31 RADIUS 38.8 39.2 39.6 40.0 40.4 40.9 41.3 41.7 42.1 42.5 42.9 43.3 BACKG 591 547 543 534 514 510 493 474 474 469 463 446 SIGMA 12 11 11 11 11 11 11 10 10 10 10 10 NREJ 32 39 32 27 29 19 31 29 18 11 11 25 RADIUS 43.7 44.1 44.5 45.0 45.4 45.8 46.2 46.6 47.0 47.4 47.8 48.2 BACKG 435 440 435 433 423 428 426 427 427 418 424 427 SIGMA 10 10 10 10 10 10 10 10 10 10 10 10 NREJ 30 27 28 27 28 17 20 17 13 29 21 22 RADIUS 48.6 49.0 49.5 49.9 50.3 50.7 51.1 51.5 51.9 52.3 52.7 53.1 BACKG 433 438 444 446 442 446 439 442 447 447 455 455 SIGMA 10 10 10 10 10 10 10 10 10 10 10 10 NREJ 18 17 23 24 20 18 21 25 27 24 17 26 RADIUS 53.6 54.0 54.4 54.8 55.2 55.6 56.0 56.4 56.8 57.2 57.7 58.1 BACKG 445 446 447 441 429 430 447 428 422 416 408 405 SIGMA 10 10 10 10 10 10 10 10 10 10 10 10 NREJ 26 19 16 19 31 30 18 30 25 17 19 18 RADIUS 58.5 58.9 59.3 59.7 60.1 60.5 60.9 61.3 61.7 62.2 62.6 63.0 BACKG 394 380 378 367 359 353 338 338 328 316 313 312 SIGMA 9 9 9 9 9 9 9 9 9 8 8 8 NREJ 19 31 21 18 18 18 29 20 27 29 18 16 RADIUS 63.4 63.8 64.2 64.6 65.0 65.4 65.8 66.3 66.7 67.1 67.5 67.9 BACKG 303 289 286 281 275 271 265 263 254 248 255 245 SIGMA 8 8 8 8 8 8 8 8 7 7 7 7 NREJ 19 30 16 20 22 24 21 17 26 28 17 22 RADIUS 68.3 68.7 69.1 69.5 69.9 70.3 70.8 71.2 71.6 72.0 72.4 72.8 BACKG 240 236 237 235 227 234 223 218 213 218 214 211 SIGMA 7 7 7 7 7 7 7 7 7 7 7 7 NREJ 25 24 18 16 25 11 19 25 31 20 20 27 RADIUS 73.2 73.6 74.0 74.4 74.9 75.3 75.7 76.1 76.5 76.9 77.3 77.7 BACKG 212 208 206 201 201 203 197 196 203 192 196 198 SIGMA 7 7 7 7 7 7 7 6 7 6 7 7 NREJ 22 27 25 26 23 17 23 24 12 26 20 14 RADIUS 78.1 78.5 79.0 79.4 79.8 80.2 80.6 81.0 81.4 81.8 82.2 82.6 BACKG 190 182 188 185 179 184 184 175 180 178 175 175 SIGMA 6 6 6 6 6 6 6 6 6 6 6 6 NREJ 21 32 24 19 31 18 16 33 22 22 23 27 RADIUS 83.0 83.5 83.9 84.3 84.7 85.1 85.5 85.9 86.3 86.7 87.1 87.6 BACKG 176 173 166 174 169 170 169 171 162 167 162 162 SIGMA 6 6 6 6 6 6 6 6 6 6 6 6 NREJ 21 27 31 18 23 25 22 17 31 23 30 31 RADIUS 88.0 88.4 88.8 89.2 89.6 90.0 90.4 90.8 91.2 91.6 92.1 92.5 BACKG 169 166 157 159 165 155 160 160 152 160 160 156 SIGMA 6 6 6 6 6 6 6 6 6 6 6 6 NREJ 15 15 26 23 17 28 19 12 28 15 15 22 RADIUS 92.9 93.3 93.7 94.1 BACKG 157 153 152 115 SIGMA 6 6 6 4 NREJ 23 25 23 12 Starting spot search... Number of spots excluded from possible ice rings: 238 Median spot size is 7 x 6 pixels, mode size is 5 by 5 Total number of spots found:1404 Number rejected as too small on X: 174 Number rejected as too small on Y: 10 Number rejected as too big on X: 64 Number rejected as too big on Y: 16 Number too close (SEPARATION keyword): 160 (currently SEPARATION 0.71 0.71) Number stored as OK: 777 highest resolution is 1.40 Angstrom 99% have resolution less than 1.52 Angstrom Number of spots found in each bin 88 32 61 168 116 25 58 110 44 17 16 53 55 15 14 40 15 3 3 14 31 2 0 11 15 1 0 10 18 0 0 18 15 0 0 2 13 0 0 19 image FILENAME: /mntdirect/_scisoft/users/svensson/WorkSpace-develop/TestCase/ref-trypsin_1_002.img Finding spots on image 2 (Midpoint of phi 90.500 degrees) Calculating radial background..... The background is radial along the X (slow) direction The average of 51 pixels, excluding outliers, is used The scan is offset by 5.8mm from the image centre in Y to avoid any backstop shadow Radial Background calculation complete RADIUS 19.1 19.6 20.0 20.4 20.8 21.2 21.6 22.0 22.4 22.8 23.2 23.7 BACKG 366 374 383 390 406 413 422 428 436 454 478 490 SIGMA 9 9 9 9 10 10 10 10 10 10 10 11 NREJ 33 30 28 28 21 25 25 33 38 31 22 27 RADIUS 24.1 24.5 24.9 25.3 25.7 26.1 26.5 26.9 27.3 27.8 28.2 28.6 BACKG 501 535 535 560 575 598 616 645 660 667 697 711 SIGMA 11 11 11 11 11 12 12 12 12 12 13 13 NREJ 35 24 35 26 30 27 36 36 34 34 27 28 RADIUS 29.0 29.4 29.8 30.2 30.6 31.0 31.4 31.8 32.3 32.7 33.1 33.5 BACKG 736 741 759 761 771 786 795 783 776 774 763 751 SIGMA 13 13 13 13 13 14 14 13 13 13 13 13 NREJ 23 28 29 30 31 29 27 31 31 26 20 21 RADIUS 33.9 34.3 34.7 35.1 35.5 35.9 36.4 36.8 37.2 37.6 38.0 38.4 BACKG 735 718 702 689 650 620 583 552 524 521 496 472 SIGMA 13 13 13 13 12 12 12 11 11 11 11 10 NREJ 24 28 30 26 21 17 30 36 38 23 24 22 RADIUS 38.8 39.2 39.6 40.0 40.4 40.9 41.3 41.7 42.1 42.5 42.9 43.3 BACKG 454 438 432 412 394 392 370 361 366 356 351 335 SIGMA 10 10 10 10 9 9 9 9 9 9 9 9 NREJ 28 29 21 29 32 22 28 28 17 25 27 36 RADIUS 43.7 44.1 44.5 45.0 45.4 45.8 46.2 46.6 47.0 47.4 47.8 48.2 BACKG 339 334 327 327 324 324 324 323 326 328 326 330 SIGMA 9 9 9 9 9 8 9 8 9 9 9 9 NREJ 24 22 26 19 26 25 28 28 25 17 23 24 RADIUS 48.6 49.0 49.5 49.9 50.3 50.7 51.1 51.5 51.9 52.3 52.7 53.1 BACKG 332 327 329 326 331 333 330 331 330 336 339 332 SIGMA 9 9 9 9 9 9 9 9 9 9 9 9 NREJ 19 22 24 25 20 21 24 28 25 24 17 29 RADIUS 53.6 54.0 54.4 54.8 55.2 55.6 56.0 56.4 56.8 57.2 57.7 58.1 BACKG 333 337 336 332 324 325 330 324 312 293 305 303 SIGMA 9 9 9 9 9 9 9 9 8 8 8 8 NREJ 28 24 20 22 31 30 29 26 23 35 23 21 RADIUS 58.5 58.9 59.3 59.7 60.1 60.5 60.9 61.3 61.7 62.2 62.6 63.0 BACKG 290 288 274 275 274 262 259 255 246 240 234 233 SIGMA 8 8 8 8 8 8 8 7 7 7 7 7 NREJ 31 28 33 26 23 31 19 20 29 26 20 16 RADIUS 63.4 63.8 64.2 64.6 65.0 65.4 65.8 66.3 66.7 67.1 67.5 67.9 BACKG 225 212 217 205 203 199 201 195 190 188 194 190 SIGMA 7 7 7 7 7 7 7 6 6 6 6 6 NREJ 20 34 15 27 26 30 17 25 30 25 21 17 RADIUS 68.3 68.7 69.1 69.5 69.9 70.3 70.8 71.2 71.6 72.0 72.4 72.8 BACKG 185 177 180 178 170 173 170 164 165 166 162 154 SIGMA 6 6 6 6 6 6 6 6 6 6 6 6 NREJ 26 32 20 26 33 19 20 30 27 17 22 32 RADIUS 73.2 73.6 74.0 74.4 74.9 75.3 75.7 76.1 76.5 76.9 77.3 77.7 BACKG 162 159 155 155 153 153 150 149 154 147 142 145 SIGMA 6 6 6 6 6 6 6 6 6 6 5 6 NREJ 14 18 30 24 19 23 29 25 14 21 27 24 RADIUS 78.1 78.5 79.0 79.4 79.8 80.2 80.6 81.0 81.4 81.8 82.2 82.6 BACKG 137 143 142 140 136 137 138 135 136 136 134 135 SIGMA 5 5 5 5 5 5 5 5 5 5 5 5 NREJ 28 26 25 32 30 26 21 28 23 24 27 26 RADIUS 83.0 83.5 83.9 84.3 84.7 85.1 85.5 85.9 86.3 86.7 87.1 87.6 BACKG 134 130 131 135 130 123 132 130 126 129 127 122 SIGMA 5 5 5 5 5 5 5 5 5 5 5 5 NREJ 28 30 24 20 24 33 18 17 26 15 20 30 RADIUS 88.0 88.4 88.8 89.2 89.6 90.0 90.4 90.8 91.2 91.6 92.1 92.5 BACKG 123 127 118 120 120 118 124 117 118 119 120 112 SIGMA 5 5 5 5 5 5 5 5 5 5 5 5 NREJ 27 14 25 27 25 28 18 28 26 21 17 34 RADIUS 92.9 93.3 93.7 94.1 BACKG 115 115 117 87 SIGMA 5 5 5 4 NREJ 23 22 20 18 Starting spot search... Number of spots excluded from possible ice rings: 283 Median spot size is 8 x 7 pixels, mode size is 6 by 6 Total number of spots found:2539 Number rejected as too small on X: 200 Number rejected as too small on Y: 106 Number rejected as too big on X: 54 Number rejected as too big on Y: 22 Number too close (SEPARATION keyword): 522 (currently SEPARATION 0.71 0.71) Number stored as OK:1052 highest resolution is 1.40 Angstrom 99% have resolution less than 1.41 Angstrom Number of spots found in each bin 110 42 36 85 125 35 44 104 104 16 15 46 70 17 22 70 72 2 1 19 37 6 1 55 186 0 0 15 38 0 1 190 224 0 0 11 24 0 0 232 FORMATTED UNKNOWN file opened on unit 10 Logical name: ref-trypsin_1.spt, Filename: ref-trypsin_1.spt 777 spots written for image 1 1052 spots written for image 2 A total of 1829 spots were written to file FORMATTED OLD file opened on unit 10 Logical name: ref-trypsin_1.spt, Filename: ref-trypsin_1.spt DPS Indexing using 848 reflections with I >= 20 I/sigma(I) DPS Indexing at Two-theta = 0.00 with 848 reflections (minimum spot separation = 0.72mm. Maximum expected cell edge 124.22, Beam position is 105.40 105.15 Generating direct lattice vectors (This may take some time): |-----------------| .................. Refining 30 direct space vectors: |----------------------------| .............................. selected 0 CELL(start) = 54.183 57.383 66.524 90.34 89.39 91.70 CELL(finis) = 54.421 57.309 66.191 90.60 89.23 92.21 Using 815 out of 848 reflections List of possible Laue groups, sorted on penalty index. The lower the PENALTY, the better No PENALTY SDCELL FRACN LATT a b c alpha beta gamma Possible spacegroups 44 999 unrefined hR 141.63 87.10 54.42 89.1 69.7 99.7 H3,H32 (hexagonal settings of R3 and R32) IN CONRHO, BAD ACOS ARG (TARRAY5) -1.1526 101.83 57.31 66.19 89.4 90.0 147.6 R3,R32 (primitive rhombohedral cell) 43 793 unrefined cI 85.12 77.49 88.00 62.4 55.4 64.6 I23,I213,I432,I4132 42 788 unrefined cF 102.00 103.40 101.83 112.1 99.0 116.0 F23,F432,F4132 41 756 unrefined tI 87.10 101.83 54.42 59.7 90.9 97.6 I4,I41,I422,I4122 40 724 unrefined mI 77.49 153.28 57.31 111.7 135.4 59.7 C2 (transformed from I2) 39 700 unrefined hR 54.42 77.49 213.05 91.2 104.7 132.4 H3,H32 (hexagonal settings of R3 and R32) 66.19 85.12 87.10 53.5 54.2 54.2 R3,R32 (primitive rhombohedral cell) 38 668 unrefined oF 54.42 124.97 142.45 81.0 111.7 113.6 F222 37 599 unrefined tI 85.12 77.49 88.00 62.4 55.4 64.6 I4,I41,I422,I4122 36 595 unrefined tI 88.00 86.26 80.54 62.9 60.5 52.8 I4,I41,I422,I4122 35 593 unrefined oI 77.49 85.12 88.00 55.4 62.4 64.6 I222,I212121 34 532 unrefined oI 54.42 87.10 101.83 82.4 59.7 89.1 I222,I212121 33 507 unrefined oF 80.54 77.49 156.09 91.4 122.0 87.0 F222 32 506 unrefined mC 80.54 77.49 85.12 64.6 115.9 87.0 C2 31 503 unrefined tI 54.42 57.31 153.82 67.8 69.1 87.8 I4,I41,I422,I4122 30 503 unrefined oI 54.42 57.31 153.82 112.2 110.9 87.8 I222,I212121 29 445 unrefined mC 124.97 54.42 87.10 89.1 126.1 66.4 C2 28 360 unrefined hP 57.31 66.19 54.42 89.2 92.2 90.6 P3,P31,P32,P312,P321,P3112,P3121,P3212,P3221 P6,P61,P65,P62,P64,P63,P622,P6122,P6522,P6222,P6422,P6322 27 270 unrefined oC 54.42 142.45 57.31 89.7 92.2 111.7 C222,C2221 26 267 unrefined mC 142.45 54.42 57.31 92.2 90.3 68.3 C2 25 257 unrefined mC 57.31 143.71 54.42 90.2 92.2 67.1 C2 24 253 unrefined hP 54.42 57.31 66.19 89.4 90.8 92.2 P3,P31,P32,P312,P321,P3112,P3121,P3212,P3221 P6,P61,P65,P62,P64,P63,P622,P6122,P6522,P6222,P6422,P6322 23 244 unrefined oC 54.42 142.45 57.31 89.7 92.2 111.7 C222,C2221 22 241 unrefined mC 142.45 54.42 57.31 92.2 90.3 68.3 C2 21 231 unrefined mC 54.42 142.45 57.31 90.3 92.2 68.3 C2 20 227 unrefined oC 54.42 124.97 66.19 90.2 90.8 113.6 C222,C2221 19 224 unrefined mC 124.97 54.42 66.19 90.8 89.8 66.4 C2 18 219 unrefined mC 54.42 124.97 66.19 89.8 90.8 66.4 C2 17 133 0.874 0.99 cP 54.42 57.31 66.19 89.4 90.8 92.2 P23,P213,P432,P4232,P4332,P4132 16 130 0.565 0.98 hR 80.54 85.12 102.00 100.0 88.4 115.9 H3,H32 (hexagonal settings of R3 and R32) 57.31 54.42 66.19 89.2 90.6 91.9 R3,R32 (primitive rhombohedral cell) 15 120 0.673 0.98 hR 77.49 85.12 105.09 98.6 87.8 115.4 H3,H32 (hexagonal settings of R3 and R32) 57.31 54.42 66.19 89.2 89.4 88.1 R3,R32 (primitive rhombohedral cell) 14 107 0.722 0.99 tP 57.31 66.19 54.42 90.8 92.2 89.4 P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212,P4322,P43212 13 104 0.474 0.98 oC 88.00 87.10 54.42 89.1 92.0 81.8 C222,C2221 12 96 0.465 0.98 mC 88.00 87.10 54.42 89.1 92.0 81.8 C2 11 93 0.465 0.98 mC 88.00 87.10 54.42 90.9 92.0 98.2 C2 10 45 0.723 0.99 tP 54.42 57.31 66.19 89.4 90.8 92.2 P4,P41,P42,P43,P422,P4212,P4122,P41212,P4222,P42212,P4322,P43212 9 36 0.501 0.98 oC 77.49 80.54 66.19 89.1 90.1 87.0 C222,C2221 8 36 0.473 0.98 mC 77.49 80.54 66.19 89.1 90.1 87.0 C2 7 26 0.449 0.98 mC 80.54 77.49 66.19 90.1 90.9 93.0 C2 6 20 0.420 0.96 oP 54.42 57.31 66.19 89.4 90.8 92.2 P222,P2221,P21212,P212121 5 17 0.517 0.98 mP 57.31 54.42 66.19 90.8 89.4 92.2 P2,P21 4 16 0.409 0.96 mP 54.42 57.31 66.19 89.4 90.8 92.2 P2,P21 3 10 0.423 0.97 mP 54.42 66.19 57.31 89.4 92.2 90.8 P2,P21 2 3 0.316 0.96 aP 54.42 57.31 66.19 89.4 90.8 92.2 P1 1 0 0.316 0.96 aP 54.42 57.31 66.19 89.4 89.2 87.8 P1 No PENALTY SDCELL FRACN LATT a b c alpha beta gamma Possible spacegroups Suggested Solution: 1 P1 penalty: 0 cell: 54.420 57.309 66.191 89.40 89.23 87.79 regularized cell: 54.420 57.309 66.191 89.40 89.23 87.79 Symmetry: aP (Triclinic) Spacegroup information obtained from library file: Logical Name: SYMINFO Filename: /opt/pxsoft/ccp4-5.99.5/lib/data/syminfo.lib Spacegroup information obtained from library file: Logical Name: SYMINFO Filename: /opt/pxsoft/ccp4-5.99.5/lib/data/syminfo.lib Mosflm has chosen solution 1 from the list automatically. You may want to re-run the autoindexing and choose a solution yourself. The solution and direct beam position will now be refined; reflections which deviate by more than the sigma cutoff from their calculated position will be excluded from the refinement. Refining solution # 1 with P1 (number 1) symmetry imposed Initial cell (before refinement) is 54.4205 57.3088 66.1914 89.403 89.228 87.788 Using 811 indexed reflections (out of 848 spots used in indexing, {delta(XY) <= 2.5 sigma}), final sd in spot positions is 0.32mm and in phi 0.78 degrees Refined cell parameters 54.68 57.40 66.22 89.33 89.11 87.02 Beam coordinates of 105.40 105.15 have been refined to 105.23 105.12 This is a shift of 0.17mm or 0.102 times the minimum spot separation of ca 1.64mm. Final cell (after refinement) is 54.6790 57.4021 66.2177 89.327 89.108 87.015 FORMATTED UNKNOWN file opened on unit 12 Logical name: autoindex.mat, Filename: autoindex.mat image FILENAME: /mntdirect/_scisoft/users/svensson/WorkSpace-develop/TestCase/ref-trypsin_1_002.img **** Information **** **** Information **** **** Information **** The cell derived from autoindexing will override that given on the CELL keyword. To force the program to use the input cell, add the keyword KEEP. eg: CELL KEEP 74.2 74.2 35.1 90 90 90 **** WARNING **** Because input wavelength ( 0.9340) is not CuKa (1.5418) or Mo (0.7107), source is assumed to be a synchrotron and synchrotron defaults for polarisation and beam divergence will be used if these have not been defined explicitly (SYNCH POLAR and DIVH/DIVV keywords. Title for MTZ and GENERATE Files (TITLE): . Crystal identifier (IDENT): ref-trypsin_1 Warning: No PROTEIN NAME given by KeyWord PNAME It has been set to "Unspecified" Warning: No CRYSTAL NAME given by KeyWord XNAME It has been set to "ref-trypsin_1" Warning: No DATASET NAME given by KeyWord DNAME It has been set to "Unspecified" PSIX changed by 0.00 Degrees and CCOMEGA set to 0.000 MAX. No. of Active Reflections= 60 Beam divergence refinement Beam divergence refinement Refining DIV with stepsize 0.01 Degrees Divergence 0.000 0.100 0.200 0.300 0.400 0.500 0.600 0.700 0.800 0.900 1.000 1.100 1.200 1.300 1.400 1.500 1.600 1.700 1.800 Divergence 1.900 2.000 No gained 0 345 386 365 329 334 325 387 318 302 307 101 100 115 112 108 129 124 138 No gained 107 113 Total intensity 49711 54184 67613 76287 79868 85225 89202 94160 96742 98521 99998 99863 99620 99373 99183 99009 98772 98477 98126 Total intensity 97882 97610 SD of intensity 134 137 167 176 178 181 186 189 190 190 191 191 191 190 190 190 190 190 190 SD of intensity 190 190 The mosaicity has been estimated as ---> 0.69 <--- for this image only; This value can be used cautiously as an initial estimate. Storing space group from DPS autoindexing: P1 number 1 Storing space group from DPS autoindexing: P1 number 1 ===> BEST OFF ===> xgui on New gui stuff switched on ===> image 1 ===> go Start and end phi values for image 1 from image header are 0.00 and 1.00 degrees. Oscillation axis set as PHI from image header ***** WARNING ***** ***** WARNING ***** ***** WARNING ***** ***** WARNING ***** Input beam coordinates 105.23mm 105.12mm DO NOT agree with those calculated from the image header ( 105.04mm 105.15mm) Warning - resetting the iseg value to zero because gui_switch = .true. image FILENAME: /mntdirect/_scisoft/users/svensson/WorkSpace-develop/TestCase/ref-trypsin_1_001.img NeoCtrl => ===> predict_spots Predicted 284 fulls 5241 partials 51 wides 264 overlaps NeoCtrl => ===> create_image binary true filename ref-trypsin_1_001.jpg Output filename set to ref-trypsin_1_001.jpg Beam centre = 105.234856 105.122574 Calling write_jpeg with arg list: trc = 0 0 blc = 2048 2048 factor = 1 write_jpeg -1 2048 2048 0 0 1 0 0 2048 2048 1 0 0 1 Rotating image by 0 degrees Done rotating write_jpeg took: 0.480 Returning from CREATE_IMAGE after 1.091 seconds NeoCtrl => ===> create_image prediction on binary true filename ref-trypsin_1_001_pred.jpg Output filename set to ref-trypsin_1_001_pred.jpg Beam centre = 105.234856 105.122574 writing binary jpeg writing predictions writing a nice binary JPEG with predictions box sizes are 8 8 zoom is 1 invert_y = 0, invert = 0, invert_x = 0 3 Rotating image by 0 degrees Done rotating Returning from CREATE_IMAGE after 1.178 seconds NeoCtrl => ===> create_image zoom -4 binary true filename ref-trypsin_1_001_small.jpg Output filename set to ref-trypsin_1_001_small.jpg Beam centre = 105.234856 105.122574 Calling write_jpeg with arg list: trc = 0 0 blc = 2048 2048 factor = -4 write_jpeg -1 2048 2048 0 0 -4 0 0 2048 2048 1 0 0 1 Rotating image by 0 degrees Done rotating write_jpeg took: 0.028 Returning from CREATE_IMAGE after 0.133 seconds NeoCtrl => ===> create_image zoom -4 prediction on binary true filename ref-trypsin_1_001_pred_small.jpg Output filename set to ref-trypsin_1_001_pred_small.jpg Beam centre = 105.234856 105.122574 writing binary jpeg writing predictions writing a nice binary JPEG with predictions box sizes are 1 1 zoom is -4 invert_y = 0, invert = 0, invert_x = 0 3 Rotating image by 0 degrees Done rotating Returning from CREATE_IMAGE after 0.151 seconds NeoCtrl => ===> return New gui stuff switched off ===> xgui off New gui stuff switched off ===> xgui on New gui stuff switched on ===> image 2 ===> go Start and end phi values for image 2 from image header are 90.00 and 91.00 degrees. Oscillation axis set as PHI from image header ***** WARNING ***** ***** WARNING ***** ***** WARNING ***** ***** WARNING ***** Input beam coordinates 105.23mm 105.12mm DO NOT agree with those calculated from the image header ( 105.04mm 105.15mm) Warning - resetting the iseg value to zero because gui_switch = .true. image FILENAME: /mntdirect/_scisoft/users/svensson/WorkSpace-develop/TestCase/ref-trypsin_1_002.img NeoCtrl => ===> predict_spots Predicted 260 fulls 5205 partials 41 wides 300 overlaps NeoCtrl => ===> create_image binary true filename ref-trypsin_1_002.jpg Output filename set to ref-trypsin_1_002.jpg binary true filename ref-trypsin_1_001_pred_small.jpg Beam centre = 105.234856 105.122574 Calling write_jpeg with arg list: trc = 0 0 blc = 2048 2048 factor = 1 write_jpeg -1 2048 2048 0 0 1 0 0 2048 2048 1 0 0 1 Rotating image by 0 degrees Done rotating write_jpeg took: 0.488 Returning from CREATE_IMAGE after 1.149 seconds NeoCtrl => ===> create_image prediction on binary true filename ref-trypsin_1_002_pred.jpg Output filename set to ref-trypsin_1_002_pred.jpg filename ref-trypsin_1_001_pred_small.jpg Beam centre = 105.234856 105.122574 writing binary jpeg writing predictions writing a nice binary JPEG with predictions box sizes are 8 8 zoom is 1 invert_y = 0, invert = 0, invert_x = 0 3 Rotating image by 0 degrees Done rotating Returning from CREATE_IMAGE after 1.209 seconds NeoCtrl => ===> create_image zoom -4 binary true filename ref-trypsin_1_002_small.jpg Output filename set to ref-trypsin_1_002_small.jpg filename ref-trypsin_1_001_pred_small.jpg Beam centre = 105.234856 105.122574 Calling write_jpeg with arg list: trc = 0 0 blc = 2048 2048 factor = -4 write_jpeg -1 2048 2048 0 0 -4 0 0 2048 2048 1 0 0 1 Rotating image by 0 degrees Done rotating write_jpeg took: 0.028 Returning from CREATE_IMAGE after 0.133 seconds NeoCtrl => ===> create_image zoom -4 prediction on binary true filename ref-trypsin_1_002_pred_small.jpg Output filename set to ref-trypsin_1_002_pred_small.jpg Beam centre = 105.234856 105.122574 writing binary jpeg writing predictions writing a nice binary JPEG with predictions box sizes are 1 1 zoom is -4 invert_y = 0, invert = 0, invert_x = 0 3 Rotating image by 0 degrees Done rotating Returning from CREATE_IMAGE after 0.150 seconds NeoCtrl => ===> return New gui stuff switched off ===> xgui off New gui stuff switched off *********** END OF PROCESSING *****************