Users are encouraged to email the
author to be informed about updates and related software.
SSIA [pdbFileName] SSIA 1IGD_H_s.pdb
SSIA D[dipolarFileName] [pdbFileName] SSIA Ddc_1igd.txt 1IGD_H_s.pdb
SSIA A[paramFileName] D[dipolarFileName] [pdbFilename] SSIA Apredict.inp Ddc_1igd.txt 1IGD_H_s.pdb
N(i) to HN(i)  0 
CA(i) to HA(i)  1 
CA(i) to CO(i)  2 
CO(i1) to N(i)  3 
CO(i1) to HN(i)  4 
2 8.17 0 3 8.27 0 2 5.60 1 3 8.98 1 2 0.61 2 3 1.05 2 2 0.82 3 3 2.11 3 2 1.61 4 3 2.93 4IMPORTANT: the sign of N(i) to HN(i) and CO(i1) to N(i) dipolar couplings has to be supplied correctly, i.e. the negative sign of the gyromagnetic ratio of 15N has to be taken into account. Therefore:
N(i) to HN(i)  isotropic  aligned 
CO(i1) to N(i)  isotropic  aligned 
CA(i) to HA(i)  aligned  isotropic 
CA(i) to CO(i)  aligned  isotropic 
CO(i1) to HN(i)  aligned  isotropic 
ANISOTROPIC_MEDIUM: 1 LIPID_CONCENTRATION: 0.05 GRID_SPACING: 0.5 DIGIT_BETA: 9 DIGIT_GAMMA: 18 DIGIT_ALPHA: 18 ATOM_RADIUS: 3.0 SELECT_FLAG: 1 PROTON_FLAG: 0 NHerror: 1.5 PRINT_EIGEN: 2
ANISOTROPIC_MEDIUM 
Bicelle/Phage selection
 
LIPID_CONCENTRATION  Total lipid/phage concentration [g/ml]  
GRID_SPACING 
Spacing of translational grid [Angstr.]
(default: 0.2)  
DIGIT_BETA 
Digitization of Euler angle beta
(180 [deg.] / DIGIT_BETA)
(default: 9)  
DIGIT_GAMMA 
Digitization of Euler angle gamma
(360 [deg.] / DIGIT_GAMMA)
(default: 18)  
DIGIT_ALPHA 
Digitization of Euler angle alpha
(360 [deg.] / DIGIT_ALPHA)
(default: 18)  
ATOM_RADIUS  Radius of atoms selected with 'SELECT_FLAG: 2' when testing for allowed orientations  
SELECT_FLAG 
Removal of part of atomic structure:
 
PROTON_FLAG 
Inclusion of protons:
 
NHerror 
Esimated error for N(i) to HN(i) dipolar couplings
used in SVD module (error is scaled for other types of dipolar
couplings)
(default: 1.5 Hz)  
PRINT_EIGEN 
Flag for printing order matrix and eigensystem:

All results are written to standard output.
When supplied with a dipolar coupling file, SSIA will predict and report two complete sets of dipolar couplings. The first set will be calculated according to the predicted sterically induced alignment tensor. The second set will be calculated according to the bestfit method of Prestegard et al. (a minimum of 5 dipolar couplings are required). This bestfit method, using order matrix analysis of residual dipolar couplings via singular value decomposition, is described in: J.A. Losonczi, M. Andrec, M.W.F. Fischer and J.H. Prestegard (1999), JMR 138, 334342.
A given alignment tensor is characterized as follows:
alpha  Clockwise rotation around z, leading to new system x',y',z' 
beta  Clockwise rotation around y', leading to new system x'',y'',z'' 
gamma  Clockwise rotation around z'' 
Statistics were computed according to methods given in:
W.H. Press, S.A. Teukolsky, B.P. Flannery and W.T. Vetterling: Numerical Recipies in C Cambridge, Cambridge University Press, 1988
1IGD_H_s.pdb  PDB file of the protein G domain (shortened by 5 residues and protons added with MOLMOL) 
dc_1igd.txt  File with measured D(NHN) dipolar couplings 
predict.inp  Configuration file 
% SSIA Ddc_1igd.txt 1IGD_H_s.pdb **  SSIA (C) M. Zweckstetter 1999  ** bicelle (1) or phage (2): 1 total lipid/phage concentration [g/ml]: 0.05 Simulation ========== Magnitude of alignment tensor ============================== Da(NH) = 8.9 [Hz] R = Dr/Da = 0.181 Orientation of alignment tensor (Euler angles [deg.] for 4 equivalent orientations) ================================================== alpha : 321.97 141.97 218.03 38.03 beta : 128.59 128.59 51.41 51.41 gamma : 48.84 48.84 228.84 228.84 Comparison of predicted residual dipolar couplings with measured ones [Hz] ========================================================================== [statistics over all dipolar couplings normalized to 1D(NH)] rmsd: 0.87 [Hz] corr r = 1.00 Q = 0.12 linear regression: offset: 0.79 +/ 0.14 [Hz] slope: 0.98 +/ 0.01 resid [DC type] predicted measured pred.  meas.      7 [0] p: 0.11 m: 1.46 diff: 1.58 8 [0] p: 7.62 m: 7.06 diff: 0.57 9 [0] p: 7.20 m: 8.65 diff: 1.45 10 [0] p: 11.08 m: 12.18 diff: 1.10 12 [0] p: 10.27 m: 12.69 diff: 2.43 13 [0] p: 4.61 m: 5.20 diff: 0.59 17 [0] p: 10.57 m: 11.68 diff: 1.11 19 [0] p: 11.14 m: 10.55 diff: 0.58 20 [0] p: 10.03 m: 11.15 diff: 1.12 21 [0] p: 10.39 m: 11.01 diff: 0.62 22 [0] p: 8.00 m: 8.87 diff: 0.87 23 [0] p: 5.51 m: 5.52 diff: 0.01 24 [0] p: 5.92 m: 5.65 diff: 0.27 25 [0] p: 4.74 m: 4.17 diff: 0.57 26 [0] p: 4.27 m: 4.80 diff: 0.53 27 [0] p: 4.71 m: 4.29 diff: 0.42 28 [0] p: 2.76 m: 2.33 diff: 0.43 29 [0] p: 15.36 m: 13.43 diff: 1.93 30 [0] p: 12.57 m: 10.60 diff: 1.97 31 [0] p: 6.84 m: 5.41 diff: 1.43 33 [0] p: 16.78 m: 16.16 diff: 0.62 35 [0] p: 8.50 m: 8.66 diff: 0.16 36 [0] p: 14.98 m: 13.97 diff: 1.01 37 [0] p: 16.67 m: 16.04 diff: 0.63 38 [0] p: 12.79 m: 12.05 diff: 0.74 39 [0] p: 10.49 m: 9.61 diff: 0.89 40 [0] p: 16.46 m: 15.70 diff: 0.77 41 [0] p: 14.87 m: 15.09 diff: 0.22 42 [0] p: 4.19 m: 3.69 diff: 0.50 43 [0] p: 6.72 m: 8.06 diff: 1.34 49 [0] p: 9.26 m: 11.68 diff: 2.41 50 [0] p: 11.00 m: 11.81 diff: 0.81 51 [0] p: 9.70 m: 10.76 diff: 1.06 52 [0] p: 10.66 m: 11.04 diff: 0.39 54 [0] p: 0.30 m: 2.46 diff: 2.16 55 [0] p: 7.47 m: 8.51 diff: 1.04 56 [0] p: 9.06 m: 9.37 diff: 0.31 57 [0] p: 10.91 m: 11.59 diff: 0.69 58 [0] p: 8.98 m: 10.15 diff: 1.17 59 [0] p: 10.07 m: 12.22 diff: 2.15 61 [0] p: 9.27 m: 11.62 diff: 2.35 17 [1] p: 21.02 m:  diff:  SVD === # of DC: 41 Predicted residual dipolar couplings not within the experimental range: Magnitude of alignment tensor ============================== Da(NH) = 9.0 [Hz] R = Dr/Da = 0.252 Orientation of alignment tensor (Euler angles [deg.] for 4 equivalent orientations) ================================================== alpha : 313.39 133.39 226.61 46.61 beta : 126.17 126.17 53.83 53.83 gamma : 53.55 53.55 233.55 233.55 Comparison of predicted residual dipolar couplings with measured ones [Hz] ========================================================================== [statistics over all dipolar couplings normalized to 1D(NH)] rmsd: 0.65 [Hz] corr r = 1.00 Q = 0.07 linear regression: offset: 0.15 +/ 0.11 [Hz] slope: 1.00 +/ 0.01 resid [DC type] predicted measured pred.  meas.      7 [0] p: 0.85 m: 1.46 diff: 0.61 8 [0] p: 6.33 m: 7.06 diff: 0.73 9 [0] p: 7.67 m: 8.65 diff: 0.98 10 [0] p: 12.10 m: 12.18 diff: 0.08 12 [0] p: 11.93 m: 12.69 diff: 0.77 13 [0] p: 5.62 m: 5.20 diff: 0.42 17 [0] p: 12.17 m: 11.68 diff: 0.50 19 [0] p: 11.96 m: 10.55 diff: 1.41 20 [0] p: 11.25 m: 11.15 diff: 0.10 21 [0] p: 11.38 m: 11.01 diff: 0.37 22 [0] p: 7.89 m: 8.87 diff: 0.98 23 [0] p: 5.40 m: 5.52 diff: 0.11 24 [0] p: 5.52 m: 5.65 diff: 0.13 25 [0] p: 4.65 m: 4.17 diff: 0.47 26 [0] p: 4.39 m: 4.80 diff: 0.41 27 [0] p: 3.73 m: 4.29 diff: 0.57 28 [0] p: 1.71 m: 2.33 diff: 0.61 29 [0] p: 14.93 m: 13.43 diff: 1.49 30 [0] p: 11.47 m: 10.60 diff: 0.87 31 [0] p: 5.78 m: 5.41 diff: 0.37 33 [0] p: 16.48 m: 16.16 diff: 0.32 35 [0] p: 7.47 m: 8.66 diff: 1.19 36 [0] p: 14.78 m: 13.97 diff: 0.81 37 [0] p: 16.14 m: 16.04 diff: 0.10 38 [0] p: 11.77 m: 12.05 diff: 0.27 39 [0] p: 9.63 m: 9.61 diff: 0.02 40 [0] p: 16.27 m: 15.70 diff: 0.57 41 [0] p: 14.00 m: 15.09 diff: 1.09 42 [0] p: 3.14 m: 3.69 diff: 0.54 43 [0] p: 8.59 m: 8.06 diff: 0.52 49 [0] p: 10.63 m: 11.68 diff: 1.05 50 [0] p: 11.50 m: 11.81 diff: 0.31 51 [0] p: 10.51 m: 10.76 diff: 0.25 52 [0] p: 11.38 m: 11.04 diff: 0.33 54 [0] p: 1.69 m: 2.46 diff: 0.76 55 [0] p: 8.58 m: 8.51 diff: 0.06 56 [0] p: 9.19 m: 9.37 diff: 0.18 57 [0] p: 11.02 m: 11.59 diff: 0.58 58 [0] p: 10.50 m: 10.15 diff: 0.35 59 [0] p: 11.66 m: 12.22 diff: 0.56 61 [0] p: 10.79 m: 11.62 diff: 0.83 17 [1] p: 23.72 m:  diff: 
C 1 C1 2 C1' 3 C1'A 4 C1'C 5 C1'N 6 C10 7 C11 8 C12 9 C13 10 C14 11 C15 12 C16 13 C17 14 C18 15 C19 16 C1A 17 C1B 18 C1C 19 C1D 20 C1M 21 C2 22 C2' 23 C2'A 24 C2'C 25 C2'N 26 C20 27 C21 28 C210 29 C211 30 C212 31 C213 32 C214 33 C215 34 C216 35 C22 36 C23 37 C24 38 C25 39 C26 40 C27 41 C28 42 C29 43 C2A 44 C2B 45 C2C 46 C2D 47 C2N 48 C3 49 C3' 50 
C3'A 51 C3'C 52 C3'N 53 C30 54 C31 55 C310 56 C311 57 C312 58 C313 59 C314 60 C315 61 C316 62 C32 63 C33 64 C34 65 C35 66 C36 67 C37 68 C38 69 C39 70 C3A 71 C3B 72 C3C 73 C3D 74 C3N 75 C4 76 C4' 77 C4'A 78 C4'C 79 C4'N 80 C40 81 C41 82 C42 83 C43 84 C44 85 C45 86 C46 87 C4A 88 C4B 89 C4C 90 C4D 91 C4N 92 C5 93 C5' 94 C5'A 95 C5'C 96 C5'N 97 C5A 98 C5C 99 C5M 100 
C5N 101 C6 102 C6A 103 C6C 104 C6N 105 C7 106 C7M 107 C7N 108 C8 109 C8A 110 C8M 111 C9 112 C9A 113 CA 114 CAA 115 CAB 116 CAC 117 CAD 118 CAL 119 CAY 120 CB 121 CB1 122 CB2 123 CBA 124 CBB 125 CBC 126 CBD 127 CC 128 CD 129 CD1 130 CD2 131 CE 132 CE1 133 CE2 134 CE3 135 CED 136 CF 137 CF3 138 CG 139 CG1 140 CG2 141 CG3 142 CGA 143 CGD 144 CH2 145 CH3 146 CHA 147 CHB 148 CHC 149 CHD 150 
CL 151 CL1 152 CLP 153 CM 154 CM1 155 CM10 156 CM2 157 CM3 158 CM4 159 CM5 160 CM6 161 CM7 162 CM8 163 CM9 164 CMA 165 CMB 166 CMC 167 CMD 168 CP1 169 CP10 170 CP11 171 CP12 172 CP13 173 CP14 174 CP15 175 CP16 176 CP17 177 CP18 178 CP19 179 CP2 180 CP20 181 CP3 182 CP4 183 CP5 184 CP6 185 CP7 186 CP8 187 CP9 188 CR 189 CRP 190 CT 191 CY 192 CZ 193 CZ2 194 CZ3 195 Cl 196 FC1 197 FC2 198 FC3 199 N1C 200 
N3C 201 N4C 202 NC 203 O2'C 204 O2C 205 O3'C 206 O4'C 207 O5'C 208 1NE2 209 1ZN 210 N 211 N1 212 N10 213 N1A 214 N1N 215 N2 216 N3 217 N3A 218 N4 219 N5 220 N6 221 N6A 222 N7 223 N7A 224 N7N 225 N9 226 N9A 227 NA 228 NB 229 ND 230 ND1 231 ND2 232 NE 233 NE1 234 NE2 235 NH1 236 NH2 237 NL 238 NR 239 NT 240 NZ 241 NZ1 242 Na 243 O1PN 244 O2'N 245 O2PN 246 O3'N 247 O4'N 248 O5'N 249 O7N 250 
PN 251 ZN 252 O 253 O1 254 O10 255 O11 256 O12 257 O13 258 O14 259 O1A 260 O1B 261 O1D 262 O1P 263 O1PA 264 O2 265 O2' 266 O2'A 267 O21 268 O22 269 O2A 270 O2D 271 O2P 272 O2PA 273 O3 274 O3' 275 O3'A 276 O31 277 O32 278 O3P 279 O4 280 O4' 281 O4'A 282 O5 283 O5' 284 O5'A 285 O6 286 O7 287 O8 288 O9 289 OBB 290 OBD 291 OD1 292 OD2 293 OE1 294 OE2 295 OF 296 OF1 297 OF2 298 OF3 299 OG 300 
OG1 301 OG2 302 OG3 303 OH 304 OH1 305 OH2 306 OH3 307 OL 308 OM 309 OR 310 OS1 311 OS2 312 OS3 313 OS4 314 OY 315 SOD 316 S 317 S2 318 S3 319 SD 320 SG 321 FE 322 MG 323 P 324 P1 325 PA 326 PF 327 YB 328 H 551 H1 330 H1' 331 H10 332 H101 333 H102 334 H10R 335 H10S 336 H10X 337 H10Y 338 H11 339 H111 340 H112 341 H113 342 H11A 343 H11B 344 H11R 345 H11S 346 H11X 347 H11Y 348 H12 349 H121 350 
H122 351 H123 352 H12A 353 H12B 354 H12R 355 H12S 356 H12T 357 H12X 358 H12Y 359 H12Z 360 H13 361 H13A 362 H13B 363 H13C 364 H13R 365 H13S 366 H13X 367 H13Y 368 H14A 369 H14B 370 H14C 371 H14R 372 H14S 373 H14T 374 H14X 375 H14Y 376 H14Z 377 H15A 378 H15B 379 H15C 380 H15R 381 H15S 382 H15X 383 H15Y 384 H16R 385 H16S 386 H16T 387 H16X 388 H16Y 389 H16Z 390 H2 391 H2' 392 H2'' 393 H2'A 394 H2'C 395 H2'N 396 H21 397 H211 398 H212 399 H213 400 
H22 401 H23 402 H2R 403 H2S 404 H2X 405 H2Y 406 H3 407 H3' 408 H3'A 409 H3'N 410 H31 411 H32 412 H33 413 H3R 414 H3S 415 H3T 416 H3X 417 H3Y 418 H4 419 H4' 420 H41 421 H41C 422 H42 423 H42C 424 H43 425 H4R 426 H4S 427 H4X 428 H4Y 429 H5 430 H5' 431 H5'' 432 H51 433 H52 434 H53 435 H5R 436 H5S 437 H5T 438 H5X 439 H5Y 440 H6 441 H61 442 H61A 443 H62 444 H62A 445 H63 446 H6R 447 H6S 448 H6X 449 H6Y 450 
H7 451 H71 452 H71N 453 H72 454 H72N 455 H73 456 H7R 457 H7S 458 H7X 459 H7Y 460 H8 461 H81 462 H82 463 H83 464 H8R 465 H8S 466 H8X 467 H8Y 468 H9 469 H91 470 H92 471 H9R 472 H9S 473 H9X 474 H9Y 475 HA 476 HA1 477 HA2 478 HA3 479 HAA1 480 HAA2 481 HAB 482 HAC 483 HAD1 484 HAD2 485 HB 486 HB1 487 HB2 488 HB3 489 HBA1 490 HBA2 491 HBB1 492 HBB2 493 HBC1 494 HBC2 495 HBD1 496 HBD2 497 HC 498 HC1 499 HC2 500 
HC3 501 HD 502 HD1 503 HD11 504 HD12 505 HD13 506 HD2 507 HD21 508 HD22 509 HD23 510 HD3 511 HE 512 HE1 513 HE2 514 HE21 515 HE22 516 HE3 517 HG 518 HG1 519 HG11 520 HG12 521 HG13 522 HG2 523 HG21 524 HG22 525 HG23 526 HG31 527 HG32 528 HH 529 HH11 530 HH12 531 HH2 532 HH21 533 HH22 534 HL 535 HL1 536 HL2 537 HL3 538 HMA1 539 HMA2 540 HMA3 541 HMB1 542 HMB2 543 HMB3 544 HMC1 545 HMC2 546 HMC3 547 HMD1 548 HMD2 549 HMD3 550 
HN 551 HN1 552 HN2 553 HN3 554 HN5 555 HO 556 HO1 557 HO2 558 HO3 559 HO4 560 HO6 561 HO7 562 HO8 563 HO9 564 HR 565 HR1 566 HR2 567 HR3 568 HS 569 HT 570 HT1 571 HT2 572 HX 573 HY 574 HY1 575 HY2 576 HY3 577 HZ 578 HZ1 579 HZ11 580 HZ12 581 HZ13 582 HZ2 583 HZ3 584 1HG 585 1HG1 586 2HG 587 2HG1 588 OXT 1 OT1 2 OT2 3 OT3 4 1HA 1000 2HA 1000 1HB 1000 2HB 1000 3HB 1000 1HG 1000 2HG 1000 1HG1 1000 2HG1 1000 3HG1 1000 1HG2 1000 2HG2 1000 3HG2 1000 1HE 1000 2HE 1000 
3HE 1000 1HE2 1000 2HE2 1000 1HD 1000 2HD 1000 1HD1 1000 2HD1 1000 3HD1 1000 1HD2 1000 2HD2 1000 3HD2 1000 1HZ 1000 2HZ 1000 3HZ 1000 1HH1 1000 2HH1 1000 1HH2 1000 2HH2 1000 1HT 1000 2HT 1000 3HT 1000 1H 330 2H 391 3H 407 X 0 QB 0 