geostas. bio3d 2.3-0

Usage

geostas(...)
"geostas"(...)
"geostas"(xyz, amsm = NULL, k = 3, pairwise = TRUE, clustalg = "kmeans", fit = TRUE, ncore = NULL, verbose=TRUE, ...)
"geostas"(nma, m.inds = 7:11, verbose=TRUE, ...)
"geostas"(enma, pdbs = NULL, m.inds = 1:5, verbose=TRUE, ...)
"geostas"(pdb, inds = NULL, verbose=TRUE, ...)
"geostas"(pdbs, verbose=TRUE, ...)
amsm.xyz(xyz, ncore = NULL)
"print"(x, ...)

Arguments

...: arguments passed to and from functions, such as kmeans, and hclust which are called internally in geostas.xyz.
xyz: numeric matrix of xyz coordinates as obtained e.g. by read.ncdf, read.dcd, or mktrj.
amsm: a numeric matrix as obtained by amsm.xyz (convenient e.g. for re-doing only the clustering analysis of the ‘AMSM’ matrix).
k: an integer scalar or vector with the desired number of groups.
pairwise: logical, if TRUE use pairwise clustering of the atomic movement similarity matrix (AMSM), else columnwise.
clustalg: a character string specifing the clustering algorithm. Allowed values are ‘kmeans’ and ‘hclust’.
fit: logical, if TRUE coordinate superposition on identified core atoms is performed prior to the calculation of the AMS matrix.
ncore: number of CPU cores used to do the calculation. ncore>1 requires package ‘parallel’ installed.
verbose: logical, if TRUE details of the geostas calculations are printed to screen.
nma: an ‘nma’ object as obtained from function nma. Function mktrj is used internally to generate a trajectory based on the normal modes.
m.inds: the mode number(s) along which trajectory should be made (see function mktrj).
enma: an ‘enma’ object as obtained from function nma.pdbs. Function mktrj is used internally to generate a trajectory based on the normal modes.
pdbs: a ‘pdbs’ object as obtained from function pdbaln or read.fasta.pdb.
pdb: a ‘pdb’ object as obtained from function read.pdb.
inds: a ‘select’ object as obtained from function atom.select giving the atomic indices at which the calculation should be based. By default the function will attempt to locate C-alpha atoms using function atom.select.
x: a ‘geostas’ object as obtained from function geostas.

Description

Identifies geometrically stable domains in biomolecules

Details

This function attempts to identify rigid domains in a protein (or nucleic acid) structure based on an structural ensemble, e.g. obtained from NMR experiments, molecular dynamics simulations, or normal mode analysis.

The algorithm is based on a geometric approach for comparing pairwise traces of atomic motion and the search for their best superposition using a quaternion representation of rotation. The result is stored in a NxN atomic movement similarity matrix (AMSM) describing the correspondence between all pairs of atom motion. Rigid domains are obtained by clustering the elements of the AMS matrix (pairwise=TRUE), or alternatively, the columns similarity (pairwise=FALSE), using either K-means (kmeans) or hierarchical (hclust) clustering.

Compared to the conventional cross-correlation matrix (see function dccm) the “geostas” approach provide functionality to also detect domains involved in rotational motions (i.e. two atoms located on opposite sides of a rotating domain will appear as anti-correlated in the cross-correlation matrix, but should obtain a high similarity coefficient in the AMS matrix).

See examples for more details.

Note

The current implementation in Bio3D uses a different fitting and clustering approach than the original Java implementation. The results will therefore differ.

Value

amsm: a numeric matrix of atomic movement similarity (AMSM).
fit.inds: a numeric vector of xyz indices used for fitting.
grps: a numeric vector containing the domain assignment per residue.
atomgrps: a numeric vector containing the domain assignment per atom (only provided for geostas.pdb).
inds: a list of atom ‘select’ objects with indices to corresponding to the identified domains.

References

Romanowska, J. et al. (2012) JCTC 8, 2588--2599. Skjaerven, L. et al. (2014) BMC Bioinformatics 15, 399. Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696.

Examples


# PDB server connection required - testing excluded

#### NMR-ensemble example
## Read a multi-model PDB file 
pdb <- read.pdb("1d1d", multi=TRUE)

  Note: Accessing on-line PDB file


## Find domains and write PDB
gs  <- geostas(pdb, fit=TRUE)

  .. 220 'calpha' atoms selected
  .. 'xyz' coordinate data with 20 frames 
  .. 'fit=TRUE': running function 'core.find'
  .. coordinates are superimposed to core region
  .. calculating atomic movement similarity matrix ('amsm.xyz()') 
  .. dimensions of AMSM are 220x220
  .. clustering AMSM using 'kmeans' 
  .. converting indices to match input 'pdb' object 
     (additional attribute 'atomgrps' generated) 


## Plot a atomic movement similarity matrix
plot.geostas(gs, contour=FALSE)

## Fit all frames to the 'first' domain
domain.inds <- gs$inds[[1]]



xyz <- pdbfit(pdb, inds=domain.inds)

#write.pdb(pdb, xyz=xyz, chain=gs$atomgrps)



#### NMA example
## Fetch stucture
pdb <- read.pdb("1crn")

  Note: Accessing on-line PDB file


## Calculate (vibrational) normal modes
modes <- nma(pdb)

 Building Hessian...		Done in 0.013 seconds.
 Diagonalizing Hessian...	Done in 0.009 seconds.


## Find domains
gs <- geostas(modes, k=2)

  .. generating trajectory from 5 modes
  .. 'xyz' coordinate data with 85 frames 
  .. 'fit=TRUE': running function 'core.find'
  .. coordinates are superimposed to core region
  .. calculating atomic movement similarity matrix ('amsm.xyz()') 
  .. dimensions of AMSM are 46x46
  .. clustering AMSM using 'kmeans' 


## Write NMA trajectory with domain assignment
mktrj(modes, mode=7, chain=gs$grps)

## Redo geostas domain clustering 
gs <- geostas(modes, amsm=gs$amsm, k=5)

  .. generating trajectory from 5 modes
  .. 'xyz' coordinate data with 85 frames 
  .. coordinates are not superimposed prior to geostas calculation
  .. clustering AMSM using 'kmeans' 





#### Trajectory example
## Read inn DCD trajectory file, fit coordinates
dcdfile <- system.file("examples/hivp.dcd", package = "bio3d")
trj <- read.dcd(dcdfile)

 NATOM = 198 
 NFRAME= 117 
 ISTART= 0 
 last  = 117 
 nstep = 117 
 nfile = 117 
 NSAVE = 1 
 NDEGF = 0 
 version 24 
Reading (x100)
  |======================================================================| 100%

xyz <- fit.xyz(trj[1,], trj)

Warning message:
No fitting indices provided, using the 198 non NA positions


## Find domains
gs <- geostas(xyz, k=3, fit=FALSE)

  .. 'xyz' coordinate data with 117 frames 
  .. coordinates are not superimposed prior to geostas calculation
  .. calculating atomic movement similarity matrix ('amsm.xyz()') 
  .. dimensions of AMSM are 198x198
  .. clustering AMSM using 'kmeans' 


## Principal component analysis 
pc.md <- pca.xyz(xyz)

## Visualize PCs with colored domains (chain ID)
mktrj(pc.md, pc=1, chain=gs$grps)




#### X-ray ensemble GroEL subunits
# Define the ensemble PDB-ids
ids <- c("1sx4_[A,B,H,I]", "1xck_[A-B]", "1sx3_[A-B]", "4ab3_[A-B]")

# Download and split PDBs by chain ID
raw.files <- get.pdb(ids, path = "raw_pdbs", gzip = TRUE)
files <- pdbsplit(raw.files, ids, path = "raw_pdbs/split_chain/")


  |======================================================================| 100%


# Align structures
pdbs <- pdbaln(files)

Reading PDB files:
raw_pdbs/split_chain//1sx4_A.pdb
raw_pdbs/split_chain//1sx4_B.pdb
raw_pdbs/split_chain//1sx4_H.pdb
raw_pdbs/split_chain//1sx4_I.pdb
raw_pdbs/split_chain//1xck_A.pdb
raw_pdbs/split_chain//1xck_B.pdb
raw_pdbs/split_chain//1sx3_A.pdb
raw_pdbs/split_chain//1sx3_B.pdb
raw_pdbs/split_chain//4ab3_A.pdb
raw_pdbs/split_chain//4ab3_B.pdb
..........

Extracting sequences

pdb/seq: 1   name: raw_pdbs/split_chain//1sx4_A.pdb 
pdb/seq: 2   name: raw_pdbs/split_chain//1sx4_B.pdb 
pdb/seq: 3   name: raw_pdbs/split_chain//1sx4_H.pdb 
pdb/seq: 4   name: raw_pdbs/split_chain//1sx4_I.pdb 
pdb/seq: 5   name: raw_pdbs/split_chain//1xck_A.pdb 
pdb/seq: 6   name: raw_pdbs/split_chain//1xck_B.pdb 
pdb/seq: 7   name: raw_pdbs/split_chain//1sx3_A.pdb 
pdb/seq: 8   name: raw_pdbs/split_chain//1sx3_B.pdb 
pdb/seq: 9   name: raw_pdbs/split_chain//4ab3_A.pdb 
pdb/seq: 10   name: raw_pdbs/split_chain//4ab3_B.pdb 


# Find domains
gs <- geostas(pdbs, k=4, fit=TRUE)

  .. 1569 non-gap positions selected
  .. 'xyz' coordinate data with 10 frames 
  .. 'fit=TRUE': running function 'core.find'
  .. coordinates are superimposed to core region
  .. calculating atomic movement similarity matrix ('amsm.xyz()') 
  .. dimensions of AMSM are 523x523
  .. clustering AMSM using 'kmeans' 


# Superimpose to core region
pdbs$xyz <- pdbfit(pdbs, inds=gs$fit.inds)

# Principal component analysis 
pc.xray <- pca(pdbs)

# Visualize PCs with colored domains (chain ID)
mktrj(pc.xray, pc=1, chain=gs$grps)


##- Same, but more manual approach 
gaps.pos <- gap.inspect(pdbs$xyz)

# Find core region
core <- core.find(pdbs)

 core size 522 of 523  vol = 6446.395 
 core size 521 of 523  vol = 6316.869 
 core size 520 of 523  vol = 6192.665 
 core size 519 of 523  vol = 6071.24 
 core size 518 of 523  vol = 5956 
 core size 517 of 523  vol = 5841.265 
 core size 516 of 523  vol = 5724.389 
 core size 515 of 523  vol = 5598.024 
 core size 514 of 523  vol = 5505.679 
 core size 513 of 523  vol = 5420.778 
 core size 512 of 523  vol = 5331.605 
 core size 511 of 523  vol = 5248.446 
 core size 510 of 523  vol = 5168.015 
 core size 509 of 523  vol = 5097.58 
 core size 508 of 523  vol = 5011.538 
 core size 507 of 523  vol = 4923.883 
 core size 506 of 523  vol = 4844.813 
 core size 505 of 523  vol = 4776.429 
 core size 504 of 523  vol = 4692.108 
 core size 503 of 523  vol = 4618.873 
 core size 502 of 523  vol = 4542.239 
 core size 501 of 523  vol = 4473.649 
 core size 500 of 523  vol = 4403.837 
 core size 499 of 523  vol = 4334.207 
 core size 498 of 523  vol = 4286.785 
 core size 497 of 523  vol = 4223.922 
 core size 496 of 523  vol = 4178.361 
 core size 495 of 523  vol = 4114.812 
 core size 494 of 523  vol = 4065.855 
 core size 493 of 523  vol = 4021.027 
 core size 492 of 523  vol = 3977.844 
 core size 491 of 523  vol = 3927.871 
 core size 490 of 523  vol = 3879.635 
 core size 489 of 523  vol = 3827.791 
 core size 488 of 523  vol = 3771.895 
 core size 487 of 523  vol = 3720.998 
 core size 486 of 523  vol = 3671.378 
 core size 485 of 523  vol = 3613.118 
 core size 484 of 523  vol = 3560.233 
 core size 483 of 523  vol = 3505.806 
 core size 482 of 523  vol = 3452.731 
 core size 481 of 523  vol = 3414.454 
 core size 480 of 523  vol = 3375.548 
 core size 479 of 523  vol = 3329.392 
 core size 478 of 523  vol = 3285.413 
 core size 477 of 523  vol = 3244.743 
 core size 476 of 523  vol = 3201.697 
 core size 475 of 523  vol = 3162.417 
 core size 474 of 523  vol = 3123.15 
 core size 473 of 523  vol = 3079.758 
 core size 472 of 523  vol = 3036.888 
 core size 471 of 523  vol = 2987.262 
 core size 470 of 523  vol = 2957.669 
 core size 469 of 523  vol = 2923.79 
 core size 468 of 523  vol = 2889.149 
 core size 467 of 523  vol = 2856.689 
 core size 466 of 523  vol = 2818.157 
 core size 465 of 523  vol = 2784.161 
 core size 464 of 523  vol = 2745.535 
 core size 463 of 523  vol = 2702.435 
 core size 462 of 523  vol = 2651.363 
 core size 461 of 523  vol = 2622.559 
 core size 460 of 523  vol = 2578.404 
 core size 459 of 523  vol = 2550.123 
 core size 458 of 523  vol = 2511.64 
 core size 457 of 523  vol = 2476.22 
 core size 456 of 523  vol = 2453.882 
 core size 455 of 523  vol = 2428.977 
 core size 454 of 523  vol = 2406.363 
 core size 453 of 523  vol = 2379.14 
 core size 452 of 523  vol = 2346.55 
 core size 451 of 523  vol = 2306.998 
 core size 450 of 523  vol = 2278.307 
 core size 449 of 523  vol = 2257.135 
 core size 448 of 523  vol = 2234.657 
 core size 447 of 523  vol = 2210.146 
 core size 446 of 523  vol = 2192.121 
 core size 445 of 523  vol = 2177.246 
 core size 444 of 523  vol = 2153.257 
 core size 443 of 523  vol = 2127.202 
 core size 442 of 523  vol = 2104.921 
 core size 441 of 523  vol = 2079.106 
 core size 440 of 523  vol = 2043.655 
 core size 439 of 523  vol = 1996.65 
 core size 438 of 523  vol = 1957.765 
 core size 437 of 523  vol = 1931.91 
 core size 436 of 523  vol = 1908.683 
 core size 435 of 523  vol = 1892.177 
 core size 434 of 523  vol = 1875.47 
 core size 433 of 523  vol = 1850.336 
 core size 432 of 523  vol = 1829.666 
 core size 431 of 523  vol = 1808.438 
 core size 430 of 523  vol = 1790.485 
 core size 429 of 523  vol = 1767.266 
 core size 428 of 523  vol = 1755.76 
 core size 427 of 523  vol = 1739.14 
 core size 426 of 523  vol = 1716.73 
 core size 425 of 523  vol = 1680.031 
 core size 424 of 523  vol = 1653.883 
 core size 423 of 523  vol = 1636.674 
 core size 422 of 523  vol = 1610.199 
 core size 421 of 523  vol = 1589.881 
 core size 420 of 523  vol = 1563.268 
 core size 419 of 523  vol = 1555.686 
 core size 418 of 523  vol = 1525.146 
 core size 417 of 523  vol = 1505.498 
 core size 416 of 523  vol = 1480.181 
 core size 415 of 523  vol = 1466.243 
 core size 414 of 523  vol = 1442.466 
 core size 413 of 523  vol = 1413.597 
 core size 412 of 523  vol = 1392.795 
 core size 411 of 523  vol = 1377.501 
 core size 410 of 523  vol = 1353.087 
 core size 409 of 523  vol = 1310.301 
 core size 408 of 523  vol = 1271.485 
 core size 407 of 523  vol = 1251.26 
 core size 406 of 523  vol = 1233.928 
 core size 405 of 523  vol = 1214.185 
 core size 404 of 523  vol = 1203.452 
 core size 403 of 523  vol = 1180.312 
 core size 402 of 523  vol = 1153.446 
 core size 401 of 523  vol = 1133.862 
 core size 400 of 523  vol = 1112.512 
 core size 399 of 523  vol = 1086.741 
 core size 398 of 523  vol = 1076.38 
 core size 397 of 523  vol = 1051.229 
 core size 396 of 523  vol = 1036.102 
 core size 395 of 523  vol = 1013.196 
 core size 394 of 523  vol = 997.744 
 core size 393 of 523  vol = 970.507 
 core size 392 of 523  vol = 964.526 
 core size 391 of 523  vol = 953.432 
 core size 390 of 523  vol = 930.833 
 core size 389 of 523  vol = 906.683 
 core size 388 of 523  vol = 891.721 
 core size 387 of 523  vol = 893.406 
 core size 386 of 523  vol = 881.972 
 core size 385 of 523  vol = 863.539 
 core size 384 of 523  vol = 849.537 
 core size 383 of 523  vol = 824.13 
 core size 382 of 523  vol = 807.908 
 core size 381 of 523  vol = 788.814 
 core size 380 of 523  vol = 768.701 
 core size 379 of 523  vol = 758.089 
 core size 378 of 523  vol = 735.51 
 core size 377 of 523  vol = 714.724 
 core size 376 of 523  vol = 696.521 
 core size 375 of 523  vol = 682.95 
 core size 374 of 523  vol = 667.834 
 core size 373 of 523  vol = 649.667 
 core size 372 of 523  vol = 626.344 
 core size 371 of 523  vol = 608.313 
 core size 370 of 523  vol = 590.196 
 core size 369 of 523  vol = 575.976 
 core size 368 of 523  vol = 560.374 
 core size 367 of 523  vol = 543.547 
 core size 366 of 523  vol = 517.475 
 core size 365 of 523  vol = 496.901 
 core size 364 of 523  vol = 474.991 
 core size 363 of 523  vol = 456.949 
 core size 362 of 523  vol = 435.764 
 core size 361 of 523  vol = 417.323 
 core size 360 of 523  vol = 396.396 
 core size 359 of 523  vol = 385.105 
 core size 358 of 523  vol = 370.818 
 core size 357 of 523  vol = 352.351 
 core size 356 of 523  vol = 334.495 
 core size 355 of 523  vol = 313.975 
 core size 354 of 523  vol = 302.539 
 core size 353 of 523  vol = 285.208 
 core size 352 of 523  vol = 276.784 
 core size 351 of 523  vol = 261.112 
 core size 350 of 523  vol = 251.034 
 core size 349 of 523  vol = 235.907 
 core size 348 of 523  vol = 219.714 
 core size 347 of 523  vol = 208.271 
 core size 346 of 523  vol = 196.145 
 core size 345 of 523  vol = 185.944 
 core size 344 of 523  vol = 177.86 
 core size 343 of 523  vol = 171.468 
 core size 342 of 523  vol = 164.953 
 core size 341 of 523  vol = 159.763 
 core size 340 of 523  vol = 154.583 
 core size 339 of 523  vol = 150.647 
 core size 338 of 523  vol = 144.884 
 core size 337 of 523  vol = 140.682 
 core size 336 of 523  vol = 137.392 
 core size 335 of 523  vol = 135.289 
 core size 334 of 523  vol = 132.499 
 core size 333 of 523  vol = 127.929 
 core size 332 of 523  vol = 125.773 
 core size 331 of 523  vol = 123.115 
 core size 330 of 523  vol = 120.798 
 core size 329 of 523  vol = 118.347 
 core size 328 of 523  vol = 116.495 
 core size 327 of 523  vol = 114.297 
 core size 326 of 523  vol = 111.803 
 core size 325 of 523  vol = 109.59 
 core size 324 of 523  vol = 107.045 
 core size 323 of 523  vol = 105.696 
 core size 322 of 523  vol = 103.604 
 core size 321 of 523  vol = 101.472 
 core size 320 of 523  vol = 99.945 
 core size 319 of 523  vol = 98.011 
 core size 318 of 523  vol = 96.056 
 core size 317 of 523  vol = 94.061 
 core size 316 of 523  vol = 92.085 
 core size 315 of 523  vol = 90.631 
 core size 314 of 523  vol = 88.889 
 core size 313 of 523  vol = 86.794 
 core size 312 of 523  vol = 85.164 
 core size 311 of 523  vol = 83.756 
 core size 310 of 523  vol = 82.212 
 core size 309 of 523  vol = 80.491 
 core size 308 of 523  vol = 79.432 
 core size 307 of 523  vol = 77.712 
 core size 306 of 523  vol = 76.762 
 core size 305 of 523  vol = 75.416 
 core size 304 of 523  vol = 74.236 
 core size 303 of 523  vol = 72.55 
 core size 302 of 523  vol = 70.953 
 core size 301 of 523  vol = 69.694 
 core size 300 of 523  vol = 68.773 
 core size 299 of 523  vol = 67.108 
 core size 298 of 523  vol = 65.748 
 core size 297 of 523  vol = 64.121 
 core size 296 of 523  vol = 62.62 
 core size 295 of 523  vol = 61.392 
 core size 294 of 523  vol = 60.138 
 core size 293 of 523  vol = 58.829 
 core size 292 of 523  vol = 57.482 
 core size 291 of 523  vol = 56.099 
 core size 290 of 523  vol = 54.915 
 core size 289 of 523  vol = 53.46 
 core size 288 of 523  vol = 52.082 
 core size 287 of 523  vol = 50.707 
 core size 286 of 523  vol = 49.531 
 core size 285 of 523  vol = 48.307 
 core size 284 of 523  vol = 47.016 
 core size 283 of 523  vol = 45.845 
 core size 282 of 523  vol = 44.418 
 core size 281 of 523  vol = 42.962 
 core size 280 of 523  vol = 41.669 
 core size 279 of 523  vol = 40.049 
 core size 278 of 523  vol = 38.45 
 core size 277 of 523  vol = 37.089 
 core size 276 of 523  vol = 35.634 
 core size 275 of 523  vol = 34.139 
 core size 274 of 523  vol = 32.483 
 core size 273 of 523  vol = 31.107 
 core size 272 of 523  vol = 29.88 
 core size 271 of 523  vol = 28.715 
 core size 270 of 523  vol = 27.409 
 core size 269 of 523  vol = 26.127 
 core size 268 of 523  vol = 24.934 
 core size 267 of 523  vol = 23.767 
 core size 266 of 523  vol = 22.672 
 core size 265 of 523  vol = 21.634 
 core size 264 of 523  vol = 20.776 
 core size 263 of 523  vol = 19.848 
 core size 262 of 523  vol = 19.073 
 core size 261 of 523  vol = 18.17 
 core size 260 of 523  vol = 17.308 
 core size 259 of 523  vol = 16.537 
 core size 258 of 523  vol = 15.811 
 core size 257 of 523  vol = 15.148 
 core size 256 of 523  vol = 14.55 
 core size 255 of 523  vol = 14.004 
 core size 254 of 523  vol = 13.54 
 core size 253 of 523  vol = 13.076 
 core size 252 of 523  vol = 12.704 
 core size 251 of 523  vol = 12.291 
 core size 250 of 523  vol = 11.884 
 core size 249 of 523  vol = 11.514 
 core size 248 of 523  vol = 11.139 
 core size 247 of 523  vol = 10.79 
 core size 246 of 523  vol = 10.417 
 core size 245 of 523  vol = 10.002 
 core size 244 of 523  vol = 9.618 
 core size 243 of 523  vol = 9.302 
 core size 242 of 523  vol = 9.032 
 core size 241 of 523  vol = 8.772 
 core size 240 of 523  vol = 8.521 
 core size 239 of 523  vol = 8.265 
 core size 238 of 523  vol = 7.983 
 core size 237 of 523  vol = 7.677 
 core size 236 of 523  vol = 7.419 
 core size 235 of 523  vol = 7.209 
 core size 234 of 523  vol = 6.977 
 core size 233 of 523  vol = 6.757 
 core size 232 of 523  vol = 6.592 
 core size 231 of 523  vol = 6.412 
 core size 230 of 523  vol = 6.224 
 core size 229 of 523  vol = 6.015 
 core size 228 of 523  vol = 5.838 
 core size 227 of 523  vol = 5.631 
 core size 226 of 523  vol = 5.426 
 core size 225 of 523  vol = 5.269 
 core size 224 of 523  vol = 5.08 
 core size 223 of 523  vol = 4.887 
 core size 222 of 523  vol = 4.715 
 core size 221 of 523  vol = 4.537 
 core size 220 of 523  vol = 4.375 
 core size 219 of 523  vol = 4.222 
 core size 218 of 523  vol = 4.087 
 core size 217 of 523  vol = 3.963 
 core size 216 of 523  vol = 3.867 
 core size 215 of 523  vol = 3.763 
 core size 214 of 523  vol = 3.638 
 core size 213 of 523  vol = 3.534 
 core size 212 of 523  vol = 3.422 
 core size 211 of 523  vol = 3.343 
 core size 210 of 523  vol = 3.268 
 core size 209 of 523  vol = 3.173 
 core size 208 of 523  vol = 3.082 
 core size 207 of 523  vol = 2.993 
 core size 206 of 523  vol = 2.912 
 core size 205 of 523  vol = 2.84 
 core size 204 of 523  vol = 2.752 
 core size 203 of 523  vol = 2.679 
 core size 202 of 523  vol = 2.595 
 core size 201 of 523  vol = 2.539 
 core size 200 of 523  vol = 2.484 
 core size 199 of 523  vol = 2.43 
 core size 198 of 523  vol = 2.377 
 core size 197 of 523  vol = 2.33 
 core size 196 of 523  vol = 2.289 
 core size 195 of 523  vol = 2.247 
 core size 194 of 523  vol = 2.203 
 core size 193 of 523  vol = 2.158 
 core size 192 of 523  vol = 2.118 
 core size 191 of 523  vol = 2.075 
 core size 190 of 523  vol = 2.037 
 core size 189 of 523  vol = 1.999 
 core size 188 of 523  vol = 1.959 
 core size 187 of 523  vol = 1.919 
 core size 186 of 523  vol = 1.878 
 core size 185 of 523  vol = 1.844 
 core size 184 of 523  vol = 1.807 
 core size 183 of 523  vol = 1.77 
 core size 182 of 523  vol = 1.735 
 core size 181 of 523  vol = 1.708 
 core size 180 of 523  vol = 1.673 
 core size 179 of 523  vol = 1.644 
 core size 178 of 523  vol = 1.609 
 core size 177 of 523  vol = 1.577 
 core size 176 of 523  vol = 1.539 
 core size 175 of 523  vol = 1.52 
 core size 174 of 523  vol = 1.495 
 core size 173 of 523  vol = 1.471 
 core size 172 of 523  vol = 1.444 
 core size 171 of 523  vol = 1.419 
 core size 170 of 523  vol = 1.39 
 core size 169 of 523  vol = 1.368 
 core size 168 of 523  vol = 1.347 
 core size 167 of 523  vol = 1.324 
 core size 166 of 523  vol = 1.3 
 core size 165 of 523  vol = 1.279 
 core size 164 of 523  vol = 1.258 
 core size 163 of 523  vol = 1.234 
 core size 162 of 523  vol = 1.211 
 core size 161 of 523  vol = 1.182 
 core size 160 of 523  vol = 1.158 
 core size 159 of 523  vol = 1.132 
 core size 158 of 523  vol = 1.105 
 core size 157 of 523  vol = 1.082 
 core size 156 of 523  vol = 1.061 
 core size 155 of 523  vol = 1.041 
 core size 154 of 523  vol = 1.02 
 core size 153 of 523  vol = 1.001 
 core size 152 of 523  vol = 0.98 
 core size 151 of 523  vol = 0.949 
 core size 150 of 523  vol = 0.931 
 core size 149 of 523  vol = 0.914 
 core size 148 of 523  vol = 0.899 
 core size 147 of 523  vol = 0.88 
 core size 146 of 523  vol = 0.867 
 core size 145 of 523  vol = 0.847 
 core size 144 of 523  vol = 0.834 
 core size 143 of 523  vol = 0.814 
 core size 142 of 523  vol = 0.797 
 core size 141 of 523  vol = 0.778 
 core size 140 of 523  vol = 0.761 
 core size 139 of 523  vol = 0.746 
 core size 138 of 523  vol = 0.732 
 core size 137 of 523  vol = 0.72 
 core size 136 of 523  vol = 0.698 
 core size 135 of 523  vol = 0.686 
 core size 134 of 523  vol = 0.668 
 core size 133 of 523  vol = 0.654 
 core size 132 of 523  vol = 0.637 
 core size 131 of 523  vol = 0.626 
 core size 130 of 523  vol = 0.611 
 core size 129 of 523  vol = 0.598 
 core size 128 of 523  vol = 0.585 
 core size 127 of 523  vol = 0.57 
 core size 126 of 523  vol = 0.554 
 core size 125 of 523  vol = 0.541 
 core size 124 of 523  vol = 0.529 
 core size 123 of 523  vol = 0.513 
 core size 122 of 523  vol = 0.496 
 FINISHED: Min vol ( 0.5 ) reached


# Fit to core region
xyz <- fit.xyz(pdbs$xyz[1, gaps.pos$f.inds],
               pdbs$xyz[, gaps.pos$f.inds],
               fixed.inds=core$xyz,
               mobile.inds=core$xyz)

# Find domains
gs <- geostas(xyz, k=4, fit=FALSE)

  .. 'xyz' coordinate data with 10 frames 
  .. coordinates are not superimposed prior to geostas calculation
  .. calculating atomic movement similarity matrix ('amsm.xyz()') 
  .. dimensions of AMSM are 523x523
  .. clustering AMSM using 'kmeans' 


# Perform PCA
pc.xray <- pca.xyz(xyz)

# Make trajectory
mktrj(pc.xray, pc=1, chain=gs$grps)

Author

Julia Romanowska and Lars Skjaerven

GeoStaS Domain Finder