IMPMC, CNRS UMR 7590 Campus Boucicaut, Université Paris 6 140 Rue de Lourmel 75015 Paris |
The batches displayed in this practical session were written for the SPIDER Unix version number 14.16 issued in 2006. These batches should run on your workstation if you possess a more recent Spider version.
;------------------------------------------------------------------------------! ; b01.mkd/hbl : CREATES FOUR ARTIFICIAL MICROGRAPHS of ;------------------------------------------------------------------------------! ; Lumbricus terrestris hemoglobin with : four micrographs with ; 120 projections with 5° angular increment of vcem011.hbl ; and applying 4 defocus values for CTF simulation ; defocus 1 = 25000 A dmic001.hbl ; defocus 2 = 32000 A dmic002.hbl ; defocus 3 = 39000 A dmic003.hbl ; defocus 4 = 36000 A dmic004.hbl ;------------------------------------------------------------------------------! MD TR ON ; ;----------( create eulerian angles to project the volume )--------------------! vo ea 5. 0.,90. 0.,60. _1 ; ;-----( Binarisation du volume à 15 Angstroems th f vcem011 vcem001 b 0.4 0.0 ; DO LB6 x90=1,4 ;-----(Creates a noisy plane to mimic cryoEM fields----------------------------! MO fantom{***x90} (1200,1600) R N ; ; Creates random eulerian angles for projection do lb1 x10=1,120 ; ud ic x10,x11,x12,x13 _1 ; x14=ran(x13) x15=x14*360. ; sd x10,x15,x12,x13 ../doc/dproj{***x90} ; lb1 ; ud ice _1 de _1 ; ;-------------( project the volume ) pj 3q vcem001 (41.) (1-120) ../doc/dproj{***x90} prj*** ; ;------------------------------------------------------------------------! do LB4 X10=1,120 ;-----( reads the coordinates of the 120 projections : UD S X10,X91,X92 dmic{***x90} X93=X91*2 X93=X93-41. x94=x92*2 x94=x94-41 ; ;-----( rescale the untilted projections between 0 & 1 and patch FS X51,X52 prj{***X10} X53=(X51-X52) AR prj{***X10} INT901 ((P1-X52)/X53) AR INT901 INT902 ((P1*0.5)+0.) PA INT902 fantom{***x90} X93,X94 ;-----( Save particles' coordinates in the untilted micrograph SD X10,x10,X93,X94 ../doc/dwin{***x90} LB4 ;-----( Delete intermediate files: de INT901 de INT902 de a prj001 LB6 ;------------------------------------------------------------------------------! ; creates the 4 CTF complexe files and apply them on the micrograph + noise ;------------------------------------------------------------------------------! x60=3.5 ; pixel size in A x61=0.5 ; Cs = 0.5 mm x62=25000. ; Defocus value in A x63=0.02508 ; lambda value for 200 kV x64=1200 ; X size of micrograph x65=1600 ; Y size of micrograph x66=1/(2*x60) ; maximum spatial frequency (1/(2*Pixel size in A) x67=0.00431 ; source size in A-1 x68=100. ; defocus spread in A x69=0 ; astigmatism and azimuth angle (both set to zero here) x70=0.07 ; amplitude contrast ratio x71=0.07 ; gaussian envelope half-width x72=-1 ; sign related to underfocus do lb5 x10=1,4 ; RR x62 25000.,32000.,39000.,36000. tf c tfc{***x10} x61 x62,x63 x64,x65 x66 x67,x68 x69,x69 x70,x71 x72 ; ft fantom{***x10} int002 ; mu int002 tfc{***x10} int003 * ; FT int003 ../micrographs/MIC{***x10} ; ip ../micrographs/MIC{***x10} ../micrographs/PIC{***x10} (600,800) ; ; x98=1/(2.*x60) tf d ../r2d/tfd{***x10} x61 x62,x63 (256) x98 x67,x68 x69,x69 x70,x71 S ; ro ../r2d/tfd{***x10} _3 ; li d _3 ../doc/dctf{***x10} r (1) lb5 ; ;-----[ delete intermediate files : de int003 de int002 de vcem001 de a fantom001 de a tfc001 en
; DAT/DAT dmic001.DAT Thu Aug 10 13:46:56 2006 0001 6 111 94 0 0 0 0 0002 6 144 287 0 0 0 0 0003 6 167 530 0 0 0 0 0004 6 349 448 0 0 0 0 0005 6 280 295 0 0 0 0 0006 6 343 121 0 0 0 0 0007 6 525 232 0 0 0 0 0008 6 499 418 0 0 0 0 0009 6 481 647 0 0 0 0 0010 6 309 722 0 0 0 0 0011 6 68 671 0 0 0 0 0012 6 67 423 0 0 0 0 0013 6 187 403 0 0 0 0 0014 6 210 155 0 0 0 0 0015 6 429 267 0 0 0 0 0016 6 486 79 0 0 0 0 0017 6 366 191 0 0 0 0 0018 6 376 325 0 0 0 0 0019 6 434 539 0 0 0 0 0020 6 315 605 0 0 0 0 0021 6 183 665 0 0 0 0 0022 6 184 766 0 0 0 0 0023 6 465 750 0 0 0 0 0024 6 386 645 0 0 0 0 0025 6 517 564 0 0 0 0 0026 6 318 534 0 0 0 0 0027 6 222 458 0 0 0 0 0028 6 62 554 0 0 0 0 0029 6 58 306 0 0 0 0 0030 6 140 183 0 0 0 0 0031 6 233 81 0 0 0 0 0032 6 310 218 0 0 0 0 0033 6 491 152 0 0 0 0 0034 6 359 35 0 0 0 0 0035 6 43 57 0 0 0 0 0036 6 53 178 0 0 0 0 0037 6 232 235 0 0 0 0 0038 6 292 379 0 0 0 0 0039 6 243 572 0 0 0 0 0040 6 134 605 0 0 0 0 0041 6 123 468 0 0 0 0 0042 6 410 388 0 0 0 0 0043 6 448 463 0 0 0 0 0044 6 498 322 0 0 0 0 0045 6 560 366 0 0 0 0 0046 6 540 490 0 0 0 0 0047 6 551 677 0 0 0 0 0048 6 433 697 0 0 0 0 0049 6 369 761 0 0 0 0 0050 6 267 654 0 0 0 0 0051 6 128 718 0 0 0 0 0052 6 69 740 0 0 0 0 0053 6 47 487 0 0 0 0 0054 6 121 365 0 0 0 0 0055 6 187 328 0 0 0 0 0056 6 239 365 0 0 0 0 0057 6 278 463 0 0 0 0 0058 6 352 261 0 0 0 0 0059 6 446 194 0 0 0 0 0060 6 425 129 0 0 0 0 0061 6 421 77 0 0 0 0 0062 6 547 102 0 0 0 0 0063 6 550 33 0 0 0 0 0064 6 282 31 0 0 0 0 0065 6 289 140 0 0 0 0 0066 6 181 39 0 0 0 0 0067 6 173 107 0 0 0 0 0068 6 102 32 0 0 0 0 0069 6 51 104 0 0 0 0 0070 6 91 242 0 0 0 0 0071 6 99 144 0 0 0 0 0072 6 174 226 0 0 0 0 0073 6 33 368 0 0 0 0 0074 6 39 609 0 0 0 0 0075 6 229 705 0 0 0 0 0076 6 262 752 0 0 0 0 0077 6 329 664 0 0 0 0 0078 6 375 709 0 0 0 0 0079 6 379 576 0 0 0 0 0080 6 442 604 0 0 0 0 0081 6 379 498 0 0 0 0 0082 6 238 510 0 0 0 0 0083 6 196 601 0 0 0 0 0084 6 357 385 0 0 0 0 0085 6 440 326 0 0 0 0 0086 6 557 286 0 0 0 0 0087 6 561 176 0 0 0 0 0088 6 485 508 0 0 0 0 0089 6 572 540 0 0 0 0 0090 6 561 614 0 0 0 0 0091 6 498 699 0 0 0 0 0092 6 529 744 0 0 0 0 0093 6 122 658 0 0 0 0 0094 6 111 525 0 0 0 0 0095 6 129 415 0 0 0 0 0096 6 32 243 0 0 0 0 0097 6 220 285 0 0 0 0 0098 6 256 188 0 0 0 0 0099 6 303 77 0 0 0 0 0100 6 457 30 0 0 0 0 0101 6 483 261 0 0 0 0 0102 6 468 377 0 0 0 0 0103 6 324 328 0 0 0 0 0104 6 253 414 0 0 0 0 0105 6 567 425 0 0 0 0 0106 6 28 701 0 0 0 0 0107 6 177 465 0 0 0 0 0108 6 402 439 0 0 0 0 0109 6 398 227 0 0 0 0 0110 6 373 84 0 0 0 0 0111 6 101 314 0 0 0 0 0112 6 86 614 0 0 0 0 0113 6 112 771 0 0 0 0 0114 6 315 774 0 0 0 0 0115 6 318 487 0 0 0 0 0116 6 232 23 0 0 0 0 0117 6 402 171 0 0 0 0 0118 6 204 553 0 0 0 0 0119 6 28 771 0 0 0 0 0120 6 222 640 0 0 0 0
; DAT/DAT dmic002.DAT Thu Aug 10 20:50:30 2006 0001 6 49 257 0 0 0 0 0002 6 510 137 0 0 0 0 0003 6 346 749 0 0 0 0 0004 6 77 608 0 0 0 0 0005 6 476 552 0 0 0 0 0006 6 386 464 0 0 0 0 0007 6 265 421 0 0 0 0 0008 6 192 420 0 0 0 0 0009 6 129 390 0 0 0 0 0010 6 187 316 0 0 0 0 0011 6 334 300 0 0 0 0 0012 6 274 191 0 0 0 0 0013 6 185 145 0 0 0 0 0014 6 142 194 0 0 0 0 0015 6 223 221 0 0 0 0 0016 6 160 254 0 0 0 0 0017 6 77 310 0 0 0 0 0018 6 130 314 0 0 0 0 0019 6 107 258 0 0 0 0 0020 6 78 201 0 0 0 0 0021 6 530 213 0 0 0 0 0022 6 409 210 0 0 0 0 0023 6 293 248 0 0 0 0 0024 6 233 275 0 0 0 0 0025 6 273 293 0 0 0 0 0026 6 241 330 0 0 0 0 0027 6 309 344 0 0 0 0 0028 6 412 353 0 0 0 0 0029 6 395 307 0 0 0 0 0030 6 360 351 0 0 0 0 0031 6 347 412 0 0 0 0 0032 6 301 394 0 0 0 0 0033 6 253 374 0 0 0 0 0034 6 196 372 0 0 0 0 0035 6 526 401 0 0 0 0 0036 6 319 577 0 0 0 0 0037 6 58 464 0 0 0 0 0038 6 48 389 0 0 0 0 0039 6 54 543 0 0 0 0 0040 6 29 687 0 0 0 0 0041 6 144 732 0 0 0 0 0042 6 78 757 0 0 0 0 0043 6 81 697 0 0 0 0 0044 6 236 755 0 0 0 0 0045 6 218 702 0 0 0 0 0046 6 296 705 0 0 0 0 0047 6 379 678 0 0 0 0 0048 6 434 734 0 0 0 0 0049 6 520 748 0 0 0 0 0050 6 476 701 0 0 0 0 0051 6 424 677 0 0 0 0 0052 6 484 653 0 0 0 0 0053 6 566 655 0 0 0 0 0054 6 524 597 0 0 0 0 0055 6 481 602 0 0 0 0 0056 6 419 620 0 0 0 0 0057 6 356 627 0 0 0 0 0058 6 375 575 0 0 0 0 0059 6 426 568 0 0 0 0 0060 6 432 503 0 0 0 0 0061 6 387 521 0 0 0 0 0062 6 338 490 0 0 0 0 0063 6 311 447 0 0 0 0 0064 6 229 464 0 0 0 0 0065 6 273 488 0 0 0 0 0066 6 307 533 0 0 0 0 0067 6 138 443 0 0 0 0 0068 6 173 476 0 0 0 0 0069 6 209 525 0 0 0 0 0070 6 246 577 0 0 0 0 0071 6 276 623 0 0 0 0 0072 6 218 649 0 0 0 0 0073 6 128 684 0 0 0 0 0074 6 173 674 0 0 0 0 0075 6 168 617 0 0 0 0 0076 6 119 630 0 0 0 0 0077 6 129 572 0 0 0 0 0078 6 181 568 0 0 0 0 0079 6 151 525 0 0 0 0 0080 6 102 524 0 0 0 0 0081 6 107 140 0 0 0 0 0082 6 54 126 0 0 0 0 0083 6 360 136 0 0 0 0 0084 6 291 125 0 0 0 0 0085 6 236 113 0 0 0 0 0086 6 75 37 0 0 0 0 0087 6 126 40 0 0 0 0 0088 6 98 83 0 0 0 0 0089 6 146 86 0 0 0 0 0090 6 217 59 0 0 0 0 0091 6 296 53 0 0 0 0 0092 6 418 76 0 0 0 0 0093 6 541 289 0 0 0 0 0094 6 474 251 0 0 0 0 0095 6 464 168 0 0 0 0 0096 6 341 205 0 0 0 0 0097 6 372 252 0 0 0 0 0098 6 495 314 0 0 0 0 0099 6 432 268 0 0 0 0 0100 6 495 449 0 0 0 0 0101 6 422 413 0 0 0 0 0102 6 565 493 0 0 0 0 0103 6 473 376 0 0 0 0 0104 6 510 508 0 0 0 0 0105 6 415 140 0 0 0 0 0106 6 357 80 0 0 0 0 0107 6 498 70 0 0 0 0 0108 6 549 90 0 0 0 0 0109 6 555 169 0 0 0 0 0110 6 291 764 0 0 0 0 0111 6 32 181 0 0 0 0 0112 6 386 32 0 0 0 0 0113 6 457 38 0 0 0 0 0114 6 461 108 0 0 0 0 0115 6 89 421 0 0 0 0 0116 6 103 476 0 0 0 0 0117 6 449 458 0 0 0 0 0118 6 230 169 0 0 0 0 0119 6 322 662 0 0 0 0 0120 6 386 725 0 0 0 0
; DAT/DAT dmic003.hbl.DAT Thu Aug 10 20:09:30 2006 0001 6 527 75 0 0 0 0 0002 6 455 195 0 0 0 0 0003 6 272 194 0 0 0 0 0004 6 372 93 0 0 0 0 0005 6 346 222 0 0 0 0 0006 6 192 51 0 0 0 0 0007 6 69 123 0 0 0 0 0008 6 152 187 0 0 0 0 0009 6 55 211 0 0 0 0 0010 6 143 270 0 0 0 0 0011 6 41 303 0 0 0 0 0012 6 161 350 0 0 0 0 0013 6 66 398 0 0 0 0 0014 6 208 435 0 0 0 0 0015 6 288 285 0 0 0 0 0016 6 426 342 0 0 0 0 0017 6 283 385 0 0 0 0 0018 6 223 304 0 0 0 0 0019 6 361 324 0 0 0 0 0020 6 421 481 0 0 0 0 0021 6 292 578 0 0 0 0 0022 6 146 540 0 0 0 0 0023 6 59 479 0 0 0 0 0024 6 71 549 0 0 0 0 0025 6 57 600 0 0 0 0 0026 6 79 650 0 0 0 0 0027 6 151 698 0 0 0 0 0028 6 217 722 0 0 0 0 0029 6 303 729 0 0 0 0 0030 6 398 721 0 0 0 0 0031 6 455 694 0 0 0 0 0032 6 511 631 0 0 0 0 0033 6 520 563 0 0 0 0 0034 6 510 479 0 0 0 0 0035 6 449 394 0 0 0 0 0036 6 366 389 0 0 0 0 0037 6 296 444 0 0 0 0 0038 6 247 479 0 0 0 0 0039 6 218 521 0 0 0 0 0040 6 185 579 0 0 0 0 0041 6 117 599 0 0 0 0 0042 6 153 639 0 0 0 0 0043 6 209 664 0 0 0 0 0044 6 272 678 0 0 0 0 0045 6 336 681 0 0 0 0 0046 6 410 668 0 0 0 0 0047 6 456 637 0 0 0 0 0048 6 462 590 0 0 0 0 0049 6 472 523 0 0 0 0 0050 6 415 534 0 0 0 0 0051 6 338 457 0 0 0 0 0052 6 381 496 0 0 0 0 0053 6 287 501 0 0 0 0 0054 6 348 544 0 0 0 0 0055 6 422 604 0 0 0 0 0056 6 359 628 0 0 0 0 0057 6 286 628 0 0 0 0 0058 6 228 614 0 0 0 0 0059 6 246 564 0 0 0 0 0060 6 546 396 0 0 0 0 0061 6 504 309 0 0 0 0 0062 6 542 259 0 0 0 0 0063 6 542 166 0 0 0 0 0064 6 463 125 0 0 0 0 0065 6 452 55 0 0 0 0 0066 6 409 123 0 0 0 0 0067 6 399 206 0 0 0 0 0068 6 402 266 0 0 0 0 0069 6 450 258 0 0 0 0 0070 6 509 222 0 0 0 0 0071 6 230 239 0 0 0 0 0072 6 182 229 0 0 0 0 0073 6 213 166 0 0 0 0 0074 6 256 118 0 0 0 0 0075 6 299 148 0 0 0 0 0076 6 357 155 0 0 0 0 0077 6 323 96 0 0 0 0 0078 6 290 49 0 0 0 0 0079 6 201 109 0 0 0 0 0080 6 153 126 0 0 0 0 0081 6 147 74 0 0 0 0 0082 6 106 136 0 0 0 0 0083 6 102 185 0 0 0 0 0084 6 101 239 0 0 0 0 0085 6 82 301 0 0 0 0 0086 6 110 366 0 0 0 0 0087 6 121 417 0 0 0 0 0088 6 117 473 0 0 0 0 0089 6 176 478 0 0 0 0 0090 6 214 367 0 0 0 0 0091 6 268 336 0 0 0 0 0092 6 319 348 0 0 0 0 0093 6 98 702 0 0 0 0 0094 6 44 718 0 0 0 0 0095 6 55 761 0 0 0 0 0096 6 107 760 0 0 0 0 0097 6 168 763 0 0 0 0 0098 6 257 764 0 0 0 0 0099 6 350 761 0 0 0 0 0100 6 447 764 0 0 0 0 0101 6 526 761 0 0 0 0 0102 6 511 704 0 0 0 0 0103 6 568 688 0 0 0 0 0104 6 558 605 0 0 0 0 0105 6 561 516 0 0 0 0 0106 6 467 447 0 0 0 0 0107 6 499 365 0 0 0 0 0108 6 91 64 0 0 0 0 0109 6 39 38 0 0 0 0 0110 6 34 161 0 0 0 0 0111 6 346 39 0 0 0 0 0112 6 398 36 0 0 0 0 0113 6 498 28 0 0 0 0 0114 6 569 32 0 0 0 0 0115 6 569 109 0 0 0 0 0116 6 512 124 0 0 0 0 0117 6 26 433 0 0 0 0 0118 6 30 655 0 0 0 0 0119 6 397 432 0 0 0 0 0120 6 559 453 0 0 0 0 0121 6 555 329 0 0 0 0
; DAT/DAT dmic004.hbl.DAT Thu Aug 10 20:15:31 2006 0001 6 65 105 0 0 0 0 0002 6 143 105 0 0 0 0 0003 6 237 116 0 0 0 0 0004 6 353 130 0 0 0 0 0005 6 477 172 0 0 0 0 0006 6 331 229 0 0 0 0 0007 6 161 228 0 0 0 0 0008 6 79 234 0 0 0 0 0009 6 87 326 0 0 0 0 0010 6 177 367 0 0 0 0 0011 6 294 366 0 0 0 0 0012 6 230 285 0 0 0 0 0013 6 423 294 0 0 0 0 0014 6 239 193 0 0 0 0 0015 6 435 80 0 0 0 0 0016 6 306 57 0 0 0 0 0017 6 293 152 0 0 0 0 0018 6 403 196 0 0 0 0 0019 6 340 311 0 0 0 0 0020 6 276 268 0 0 0 0 0021 6 147 497 0 0 0 0 0022 6 201 511 0 0 0 0 0023 6 265 525 0 0 0 0 0024 6 345 534 0 0 0 0 0025 6 420 542 0 0 0 0 0026 6 502 553 0 0 0 0 0027 6 482 476 0 0 0 0 0028 6 397 464 0 0 0 0 0029 6 335 463 0 0 0 0 0030 6 260 445 0 0 0 0 0031 6 208 439 0 0 0 0 0032 6 132 421 0 0 0 0 0033 6 69 414 0 0 0 0 0034 6 63 459 0 0 0 0 0035 6 55 547 0 0 0 0 0036 6 89 624 0 0 0 0 0037 6 190 634 0 0 0 0 0038 6 147 575 0 0 0 0 0039 6 261 586 0 0 0 0 0040 6 209 575 0 0 0 0 0041 6 250 634 0 0 0 0 0042 6 319 609 0 0 0 0 0043 6 385 588 0 0 0 0 0044 6 441 599 0 0 0 0 0045 6 492 608 0 0 0 0 0046 6 544 618 0 0 0 0 0047 6 297 659 0 0 0 0 0048 6 355 652 0 0 0 0 0049 6 191 719 0 0 0 0 0050 6 133 685 0 0 0 0 0051 6 80 714 0 0 0 0 0052 6 35 658 0 0 0 0 0053 6 258 716 0 0 0 0 0054 6 371 731 0 0 0 0 0055 6 472 721 0 0 0 0 0056 6 409 669 0 0 0 0 0057 6 476 664 0 0 0 0 0058 6 540 676 0 0 0 0 0059 6 563 751 0 0 0 0 0060 6 430 759 0 0 0 0 0061 6 301 765 0 0 0 0 0062 6 318 717 0 0 0 0 0063 6 236 387 0 0 0 0 0064 6 362 398 0 0 0 0 0065 6 417 401 0 0 0 0 0066 6 474 406 0 0 0 0 0067 6 539 412 0 0 0 0 0068 6 557 473 0 0 0 0 0069 6 387 347 0 0 0 0 0070 6 373 259 0 0 0 0 0071 6 255 329 0 0 0 0 0072 6 307 417 0 0 0 0 0073 6 446 350 0 0 0 0 0074 6 502 350 0 0 0 0 0075 6 558 349 0 0 0 0 0076 6 472 301 0 0 0 0 0077 6 527 297 0 0 0 0 0078 6 426 243 0 0 0 0 0079 6 481 246 0 0 0 0 0080 6 343 183 0 0 0 0 0081 6 370 78 0 0 0 0 0082 6 414 135 0 0 0 0 0083 6 498 107 0 0 0 0 0084 6 539 166 0 0 0 0 0085 6 543 227 0 0 0 0 0086 6 562 101 0 0 0 0 0087 6 532 45 0 0 0 0 0088 6 477 46 0 0 0 0 0089 6 187 157 0 0 0 0 0090 6 127 170 0 0 0 0 0091 6 62 170 0 0 0 0 0092 6 126 276 0 0 0 0 0093 6 179 302 0 0 0 0 0094 6 117 369 0 0 0 0 0095 6 104 52 0 0 0 0 0096 6 45 48 0 0 0 0 0097 6 174 52 0 0 0 0 0098 6 234 49 0 0 0 0 0099 6 50 280 0 0 0 0 0100 6 37 348 0 0 0 0 0101 6 124 748 0 0 0 0 0102 6 234 765 0 0 0 0 0103 6 102 524 0 0 0 0 0104 6 553 552 0 0 0 0 0105 6 29 737 0 0 0 0 0106 6 77 776 0 0 0 0 0107 6 314 104 0 0 0 0 0108 6 403 32 0 0 0 0 0109 6 210 238 0 0 0 0 0110 6 285 207 0 0 0 0 0111 6 502 767 0 0 0 0 0112 6 351 771 0 0 0 0 0113 6 178 768 0 0 0 0 0114 6 225 677 0 0 0 0 0115 6 138 635 0 0 0 0 0116 6 95 573 0 0 0 0 0117 6 304 557 0 0 0 0 0118 6 304 500 0 0 0 0 0119 6 463 525 0 0 0 0 0120 6 30 218 0 0 0 0
;-----------------------------------------------------------------! ; b17.fed/hbl : batch for boxing images from the SPIDER image ;-----------------------------------------------------------------! x99=1. ; Number of the micrograph ; PARAMETERS x76=120 ; last image number x81=100. ; image dimension x82=x81/2. ; 1/2 image dimension ; INPUTS: fr l [coords]../doc/dmic00{*x99} ; image coords (from WEB) fr l [micrograph]../micrographs/MIC00{*x99} ; untilted micrograph ; OUTPUTS: fr l [images]../images/win{*x99}{***x10} ; windowed images ; END BATCH HEADER ;-----------------------------------------------------------------! md tr on do lb2 x99=1,4 ; IF WEB HAS THIS BUG WITH FILES.DAT rather than FILES.hbl ;vm ;cp ../doc/dmicd00{*x99}.DAT ../doc/dmic00{*x99}.hbl ;-----[ Starts the do loop of the boxing : do lb1 x10=1,x76 ; reads central X and Y coordinates for each particle in the micrograph ud x10,x11,x12 [coords] x11=x11*2 x12=x12*2 ; subtract 1/2 image dimension from center coordinates X11=X11-x82 X12=X12-x82 ; boxing out of each particle in a set of small images wi [micrograph] [images] x81,x81 X11,X12 lb1 lb2 en
;-----------------------------------------------------------------! ; b18.fed/hbl : calculates average power spectrum of a micrograph ;-----------------------------------------------------------------! x99=2. ; Number of micrograph ; PARAMETERS: x31=512. ; window size of small pieces (Sx=Sy) x36=50. ; % of the overlap in X x37=50. ; % of the overlap in Y x56=512. ; dist. from the edge (X) x59=512. ; dist. from the edge (Y) ; INPUTS: fr l [mic]../micrographs/MIC ; micrograph ; OUTPUTS: fr l [spectrum]../r2d/pow ; power spectrum fr l [doc]../doc/dpws ; radial profile docfile ; END BATCH HEADER ;-----------------------------------------------------------------! md tr on FI x23,x24 ; gets dimensions of the full image [mic]{***x99} (12,2) ; x31 = large window size ; x87=((x23-2*x56)*(x24-2*x59))number of pieces in this micrograph x38=100/(100-x36) ; normalization of % of X overlap x39=100/(100-x37) ; normalization of % of Y overlap x26=INT(x38*((x23-2*x56)/x31-1)+1) ; number of pieces (X) x29=INT(x39*((x24-2*x59)/x31-1)+1) ; number of pieces (Y) x94=0. ;---------------------( Loops over X and Y )---------------------! do lb2 x12=1,x29 x21=(x31/x39)*(x12-1)+x59 ; Y-direction do lb3 x13=1,x26 x22=(x31/x38)*(x13-1)+x56 ; X-direction wi [mic]{***x99} ; get small pieces of the input image _5 x31,x31 ; size of small pieces x22,x21 ; coordinates of the upper left corner ra ; correct ramp effects _5 _6 pw ; calculates power spectrum of each small piece _6 _7 wu _7 _8 x94=x94+1 if (x94.ge.2) then ad _3 _8 _3 * else cp _8 _3 endif lb3 lb2 cp ; write the output file _8 [spectrum]{***x99} ; create the document file, with column headings and spatial freq. column ro _8 _9 ; 1D rotational average li d _9 _10 r (1) ; labels for columns in output file SD / amplitude x-axis spat.freq. [doc]{***x99} x71 = x31/2 ; 1/2 large window size do lb5 x70=1,x71 ud ic,x70,x72,x73 _10 x74=x70/(2.0*x71) ; computes spat.frequencies sd x70,x72,x73,x74 [doc]{***x99} lb5 ud ice _10 en
;---------------------------------------------------------------------------! ; b11.fed/hbl : Creating symmetry document files taking into account ; the D6 point-group symmetry of Lumbricus hemoglobin : ;---------------------------------------------------------------------------! md tr on ; OUTPUTS: fr l [top_sym]../doc/d6top ; top-view symmetry doc file fr l [side_sym]../doc/d6side ; side-view symmetry doc file ; END BATCH HEADER ; D6 Symmetry for hexagonal top views ; 6-fold axis parallel to Z axis) do lb1 x10=1,12 rr x11 0.0,0.0,0.0,0.0,0.0,0.0,0.0,60.,120.,180.,240.,300. rr x12 0.0,0.0,0.0,0.0,0.0,0.0,180.,180.,180.,180.,180.,180. rr x13 0.0,60.,120.,180.,240.,300.,0.0,0.0,0.0,0.0,0.0,0.0 sd x10,x13,x12,x11 [top_sym] lb1 ; D6 Symmetry for rectangular side views ; (6-fold axis parallel to Y axis) do lb2 x20=1,12 rr x11 0.0,0.0,0.0,0.0,0.0,0.0,180.0,180.0,180.0,180.,180.,180. rr x12 0.0,60.0,120.,180.,240.,300.,0.0,60.,120.,180.,240.,300. rr x13 0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0 sd x20,x13,x12,x11 [side_sym] lb2 en d
;------------------------------------------------------------------------! ; b19.fed/hbl : Creates a 3D mask and selection docfiles for computing ; the odd and even volumes and resolution limits at each ; alignment cycle. It also creates the first reference ; volume low-pass filtered to 35A resolution. ;------------------------------------------------------------------------! x99=1. ; PARAMETERS: x79=120. ; number of images ; INPUTS: FR L [vol]../r3d/vref ; current volume ; OUTPUTS: FR L [oddsel]../doc/dodd ; Selection docfile (odd) FR L [evensel]../doc/deven ; Selection docfile (even) FR L [mask]../r3d/mask ; Mask FR L [seltotal]../doc/seltot01 ; Output file ; END BATCH HEADER ;-----------------------------------------------------------------------! md tr on DOC CREATE [seltotal] (1) (1-x79) DOC SPLIT [seltotal] [oddsel] [evensel] ; low-pass filter the first reference volume to 35A resolution fq ../makedata/vcem011 ttt 5 0.1 0.01 pd ttt [vol]01 (100,100,100) B (11,11,11) de ; Prepare the mask for 3D FSC estimation of resolution : ; Masks half-volumes TH M [vol]01 _1 B (0.305) ; FQ NP _1 _2 (5) (0.1) (0.01) ; TH M _2 _3 B (0.045) ; FQ NP _3 _4 (5) (0.1) (0.01) ; TH M _4 _5 B (0.5) ; FQ NP _5 [mask] (5) (0.1) (0.02) en
;------------------------------------------------------------------------! ; b20.fed/hbl : Reference-based alignment with SPIDER operation AP REF ;------------------------------------------------------------------------! ; PARAMETERS: x74=1. ; First cycle number x75=3. ; Last cycle number x79=120. ; number of images x56=47. ; radius of projection of the volume x55=24 ; alignment shift (pixels) for AP REF x54=5 ; first ring x98=x56-2. ; last ring for AP REF x97=1. ; 1st reference volume copy x14=0.1429 ; Nyquist frequency ; INPUTS: FR L [vol]../r3d/vref ; current volume FR L [unaligned_images]../images/win{*x99} ; unaligned images (no stack!) FR L [dsym]../doc/d6top ; Symmetry docfile FR L [oddsel]../doc/dodd ; Selection docfile (odd) FR L [evensel]../doc/deven ; Selection docfile (even) FR L [seltotal]../doc/seltot01 ; Selection docfile FR L [mask]../r3d/mask ; Mask ; OUTPUTS: FR L [iter_ang_voea]../doc/angvoea{**x76} ; angle voea file FR L [iter_select_voea]../doc/selvoea{**x76} ; angle voea selection file FR L [temp_ref_projs]../images/refproj{**x76} ; volume projections at each cycle FR L [next_align]../doc/align{*x99}{**x76} ; align output file FR L [align]../doc/align{*x99}{**x96} ; previous cycle align docfile FR L [next_aligned_images]../images/ali{*x99}{**x76} ; next aligned images FR L [aligned_images]../images/ali{*x99}{**x96} ; current aligned images FR L [next_vol]../r3d/vol{*x99}{***x76} ; next volume FR L [oddvol]../r3d/odd{*x99} ; odd volume FR L [evenvol]../r3d/even{*x99} ; even volume FR L [nextd]../doc/dresol{*x99} ; resolution docfile ; END BATCH HEADER ;-----------------------------------------------------------------------! md tr on do lb9 x99=1,4 ; Inquires if files exist IQ FI x88 [iter_ang_voea] IF (x88.EQ.1) THEN DE [iter_ang_voea] ENDIF ; IQ FI x88 [iter_select_voea] IF (x88.EQ.1) THEN DE [iter_select_voea] ENDIF ;cp ;../r3d/vtot01 ;[vol]{**x97} ; Cycles to be done DO LB1 x76=x74,x75 x86=x76+1 ; defines following cycle x96=x76-1 ; defines previous cycle to delete big files RR x42 ; angular restriction 0.,0.,0. RR x41 ; delta theta for projection 12.,8.,5. IQ FI x88 [temp_ref_projs] IF (x88.EQ.1) THEN DE [temp_ref_projs] ENDIF ; VO EA creates angular document file VO EA,x53 x41 ; angular step for the theta angles (0.,90.) ; Range of theta angle: (0.,60.) ; Range of phi angle [iter_ang_voea] ; ref angle doc file DOC CREATE [iter_select_voea] ; output document file (1) ; column number to be filled (1-x53) ; Values to be placed in the specified column ; Projection of the volume PJ 3Q [vol]{**x76} x56 ; radius of the object [iter_select_voea] [iter_ang_voea] [temp_ref_projs]@****** IF(x76.EQ.1) THEN ; cycle 1: non-cumulative parameters AP REF [temp_ref_projs]@****** (1-x53) x55 ; shift search range (x54,x98,1) ; first, last ring and skip [iter_ang_voea] ; ref angles (input) SCR_{**x76} ; no scratch file if fits in-core [unaligned_images]*** (1-x79) * ; no previous cycle => no previous alignment doc file x42 (1) ; check mirrored projections [next_align] ; output : alignment doc file ELSE ; if we do not start from beginning (if there were previous cycles): cumulative parameters AP REF [temp_ref_projs]@****** (1-x53) x55 ; shift search range (x54,x98,1) ; first, last ring and skip [iter_ang_voea] ; ref angles (input) SCR_{**x76} ; no scratch file if fits in-core [aligned_images]**** ; current aligned images (1-x79) ; all the images [align] ; here previous cycle => previous alignment doc file x42 (1) ; check mirrored projections [next_align] ; output : alignment doc file ENDIF ; Creates rotated and shifted images from this cycle ; Retrieve new alignment file data (just created above) DO LB6 x21=1,x79 ; PSI,THE,PHI, REF#,EXP#, ANG,SX,SY, NPROJ,DIFF,CCROT UD IC,x21, x80,x80,x80, x81,x80, x61,x62,x63, x80,x12,x31 [next_align] ; Doc file just created by 'AP REF' ; Apply combined transformation to original exp. sample image IF (x81.GE.0) THEN ; No mirror RT SQ ; Rotate & shift [unaligned_images]{***x21} ; Unaligned original images (stack) [next_aligned_images]{****x21} ; Current aligned images (output) x61 ; Inplane rotation angle x62,x63 ; Shifts ELSE ; Mirrored RT SQ ; Rotate & shift [unaligned_images]{***x21} ; Unaligned original image _1 ; Temp. output file x61 ; Inplane rotation angle x62,x63 ; Shifts MR ; Mirror _1 ; Rotated, unaligned original image [next_aligned_images]{****x21} ; Current aligned images (output) Y ; Around Y axis ENDIF LB6 ; Close doc files UD ICE [next_align] ; Finished with align. doc file ; 3D reconstruction BP 3F [next_aligned_images]**** [seltotal] [next_align] [dsym] [next_vol] ; Calculates half-volumes BP 3F [next_aligned_images]**** [oddsel] [next_align] [dsym] _11 BP 3F [next_aligned_images]**** [evensel] [next_align] [dsym] _12 MU _11 [mask] [oddvol]{**x76} * PD [oddvol]{**x76} _21 (256,256,256) b (79,79,79) MU _12 [mask] [evenvol]{**x76} * PD [evenvol]{**x76} _22 (256,256,256) b (79,79,79) ; Resolution calculation RF 3 x69,x37 ; Phase Residual & Fourier shell correlation _21 ; Odd volume _22 ; Even volume (0.5) ; Ring width (0.2,2.0) ; Scale factor C ; Missing cone/wedge angle (90.0) ; Maximum tilt angle (10.4) ; Factor for noise comparison [nextd]{**x76} ; Resolution doc file ; Calculates resolution x66=0.5/(x14*x37) IF (x76.EQ.1) THEN SD / Iteration resolution [next] ENDIF SD x76,x76,x66,x37 [nextd]{**x76} FQ NP [next_vol] _22 (5) ; 5: Fermi low-pass x37 ; at the resolution limit just measured (0.02) ; Volume centration CG PH,X11,X12,X13,X21,X22,X23 _22 X21=-X21 X22=-X22 X23=-X23 SH 3 _22 [vol]{**x86} x21,x22,x23 lb1 lb9 en
;------------------------------------------------------------------------! ; b21.fed/hbl : Wiener filtering on the 4 defocus groups ; Merging and estimation of FSC ;------------------------------------------------------------------------! ; PARAMETERS: x14=0.1429 ; Nyquist frequency x60=3.5 ; pixel size in A x61=0.5 ; Cs = 0.5 mm x62=25000. ; Defocus value in A x63=0.02508 ; lambda value for 200 kV x66=1/(2*x60) ; maximum spatial frequency (1/(2*Pixel size in A) x67=0.00431 ; source size in A-1 x68=100. ; defocus spread in A x69=0 ; astigmatism and azimuth angle (both set to zero here) x70=0.07 ; amplitude contrast ratio x71=0.07 ; gaussian envelope half-width x72=-1 ; sign related to underfocus x86=3. ; number of cycles performed x99=4 ; number of micrographs ; INPUTS: FR L [mask]../r3d/mask ; Mask FR L [oddvol]../r3d/odd{*x99} ; odd volume FR L [evenvol]../r3d/even{*x99} ; even volume ; OUTPUTS: FR L [ctf_template]../r3d/ctf{**x99} ; ctf template for Wiener filtering FR L [next_vol]../r3d/vol{*x99}*** ; raw volume FR L [next_val]../r3d/vctf{***x86} ; ctf corrected global volume FR L [nextodd]../r3d/vctfodd{***x86} ; ctf corrected odd volume FR L [nexteven]../r3d/vctfeven{***x86} ; ctf corrected even volume FR L [nextctf]../doc/dctfresol{***x86} ; ctf corrected resolution docfile ; END BATCH HEADER ;-----------------------------------------------------------------------! md tr on do lb1 x99=1,4 RR x62 25000.,32000.,39000.,36000. TF C3 [ctf_template] x61 x62,x63 (100.) x66 x67,x68 x69,x69 x70,x71 x72 cp ../r3d/vol{*x99}{***x86} ../r3d/int{***x99} cp ../r3d/odd{*x99}{**x86} ../r3d/odd{***x99} cp ../r3d/even{*x99}{**x86} ../r3d/even{***x99} lb1 TF CTS ; Transfer Function - CTF correction ../r3d/int*** ; Template for 3D volumes (input) (1-4) ; Group Selection File (input) [ctf_template] ; Template for 3D ctf file (input) (0.5) ; SNR [next_val] ; CTF corrected volume (output) TF CTS ; Transfer Function - CTF correction ../r3d/odd*** ; Template for 3D odd volumes (input) (1-4) ; Group Selection File (input) [ctf_template] ; Template for 3D ctf files - work/ctf (input) (0.5) ; SNR [nextodd] ; Odd volume (output) TF CTS ; Transfer Function - CTF correction ../r3d/even*** ; Template for 3D even volumes (input) (1-4) ; Group Selection File (input) [ctf_template] ; Template for 3D ctf files - work/ctf (input) (0.5) ; SNR [nexteven] ; Even output volume (output) MU [nextodd] [mask] _11 * PD _11 _21 (256,256,256) b (79,79,79) MU [nexteven] [mask] _12 * PD _12 _22 (256,256,256) b (79,79,79) ; Resolution calculation RF 3 x69,x37 ; Phase Residual & Fourier shell correlation _21 ; Odd volume _22 ; Even volume (0.5) ; Ring width (0.2,2.0) ; Scale factor C ; Missing cone/wedge angle (90.0) ; Maximum tilt angle (10.4) ; Factor for noise comparison [nextctf] ; Global resolution doc file ; Calculates resolution x66=0.5/(x14*x37) IF (x86.EQ.1) THEN SD / Iteration resolution [nextctf] ENDIF SD x86,x86,x66,x37 [nextctf] en
;------------------------------------------------------------------------! ; b22.fed/hbl : Wiener filtering on the 4 defocus groups ; Merging and estimation of FSC ; when no flaw of alignment or CTF estimation ; limit the efficiency of Wiener filtering ;------------------------------------------------------------------------! md tr on ; ; PARAMETERS: x14=0.1429 ; Nyquist frequency x60=3.5 ; pixel size in A x61=0.5 ; Cs = 0.5 mm x62=25000. ; Defocus value in A x63=0.02508 ; lambda value for 200 kV x66=1/(2*x60) ; maximum spatial frequency (1/(2*Pixel size in A) x67=0.00431 ; source size in A-1 x68=100. ; defocus spread in A x69=0 ; astigmatism and azimuth angle (both set to zero here) x70=0.07 ; amplitude contrast ratio x71=0.07 ; gaussian envelope half-width x72=-1 ; sign related to underfocus x86=4. ; number of cycles performed x99=4 ; number of micrograph x76=1. ; constante ; INPUTS: FR L [mask]../r3d/mask ; Mask do lb1 x10=1,4 ; 3D reconstruction BP 3F ../images/win{*x10}*** ../doc/seltot01 ../doc/dproj{***x10} ../doc/d6top ../r3d/volraw{***x10} ; Calculates half-volumes BP 3F ../images/win{*x10}*** ../doc/dodd ../doc/dproj{***x10} ../doc/d6top ../r3d/volrawodd{***x10} BP 3F ../images/win{*x10}*** ../doc/deven ../doc/dproj{***x10} ../doc/d6top ../r3d/volraweve{***x10} MU ../r3d/volrawodd{***x10} [mask] _11 * PD _11 _21 (256,256,256) b (79,79,79) MU ../r3d/volraweve{***x10} [mask] _12 * PD _12 _22 (256,256,256) b (79,79,79) ; Resolution calculation RF 3 x69,x37 ; Phase Residual & Fourier shell correlation _21 ; Odd volume _22 ; Even volume (0.5) ; Ring width (0.2,2.0) ; Scale factor C ; Missing cone/wedge angle (90.0) ; Maximum tilt angle (10.4) ; Factor for noise comparison ../doc/dresvolraw{***x10} ; Resolution doc file ; Calculates resolution x66=0.5/(x14*x37) SD / Iteration resolution ../doc/dresvolraw{***x10} SD x76,x76,x66,x37 ../doc/dresvolraw{***x10} de _11 de _12 lb1 ;--------------------------------------------------------------- TF CTS ; Transfer Function - CTF correction ../r3d/volraw*** ; Template for 3D volumes (1-4) ; Group Selection File ../r3d/ctf** ; Template for 3D ctf file (0.5) ; SNR ../r3d/volctftot ; CTF corrected volume TF CTS ; Transfer Function - CTF correction ../r3d/odd*** ; Template for 3D odd volumes (1-4) ; Group Selection File ../r3d/ctf** ; Template for 3D ctf files (0.5) ; SNR ../r3d/volctfoddtot ; Odd volume TF CTS ; Transfer Function - CTF correction ../r3d/even*** ; Template for 3D even volumes (1-4) ; Group Selection File ../r3d/ctf** ; Template for 3D ctf files (0.5) ; SNR ../r3d/volctfevetot ; Even output volume MU ../r3d/volctfoddtot [mask] _11 * PD _11 _21 (256,256,256) b (79,79,79) MU ../r3d/volctfevetot [mask] _12 * PD _12 _22 (256,256,256) b (79,79,79) ; Resolution calculation RF 3 x69,x37 ; Phase Residual & Fourier shell correlation _21 ; Odd volume _22 ; Even volume (0.5) ; Ring width (0.2,2.0) ; Scale factor C ; Missing cone/wedge angle (90.0) ; Maximum tilt angle (10.4) ; Factor for noise comparison ../doc/dresvolctftot ; Global resolution doc file ; Calculates resolution x66=0.5/(x14*x37) SD / Iteration resolution ../doc/dresvolctftot SD x76,x76,x66,x37 ../doc/dresvolctftot en
;------------------------------------------------------------------------------! ; b23.fed/hbl : CREATES FOUR ARTIFICIAL POWER SPECTRUM PROFILES ;------------------------------------------------------------------------------! ; defocus 1 = 25000 A dapws001.hbl ; defocus 2 = 32000 A dapws002.hbl ; defocus 3 = 39000 A dapws003.hbl ; defocus 4 = 36000 A dapws004.hbl ;------------------------------------------------------------------------------! MD TR ON ; ;------------------------------------------------------------------------------! ; creates the 4 CTF complexe files and apply them on the micrograph + noise ;------------------------------------------------------------------------------! x60=3.5 ; pixel size in A x61=0.5 ; Cs = 0.5 mm x62=25000. ; Defocus value in A x63=0.02508 ; lambda value for 200 kV x64=1200 ; X size of micrograph x65=1600 ; Y size of micrograph x66=1/(2*x60) ; maximum spatial frequency (1/(2*Pixel size in A) x67=0.00431 ; source size in A-1 x68=100. ; defocus spread in A x69=0 ; astigmatism and azimuth angle (both set to zero here) x70=0.07 ; amplitude contrast ratio x71=0.07 ; gaussian envelope half-width x72=-1 ; sign related to underfocus do lb5 x10=1,4 ; RR x62 25000.,32000.,39000.,36000. ; x98=1/(2.*x60) tf d ../r2d/int001 x61 x62,x63 (512) x98 x67,x68 x69,x69 x70,x71 D ; ro ../r2d/int001 _3 ; li d _3 ../doc/dapws{***x10} r (1) lb5 ; ;-----[ delete intermediate files : de int001 ; en