- edited description
bug in choosing the core (print(core, vol=))?
Hi,
I am using core.find to find the core structure for further structural alignment. But I failed to choose the core size as I wanted. The outputs of core.find seem inconsistent with print(core, vol=?). I pasted the outputs as below:
> core <- core.find(MDtrjdcd[frames, ca.ind], shortcut=TRUE, ncore=4, outpath="core_pruned", write.pdbs=TRUE, rm.island=TRUE, verbose=TRUE)
core size 1012 of 1016 vol = 135981.6
core size 1008 of 1016 vol = 113579.6
core size 1002 of 1016 vol = 81574.14
core size 998 of 1016 vol = 65388.23
core size 994 of 1016 vol = 52782.13
core size 990 of 1016 vol = 43814.84
core size 986 of 1016 vol = 38311.73
core size 982 of 1016 vol = 36061.78
core size 978 of 1016 vol = 34732.86
core size 973 of 1016 vol = 33272.91
core size 969 of 1016 vol = 32225.66
core size 964 of 1016 vol = 30926.78
core size 957 of 1016 vol = 29279.95
core size 952 of 1016 vol = 28157.97
core size 947 of 1016 vol = 27143.65
core size 943 of 1016 vol = 26380.79
core size 939 of 1016 vol = 25639.99
core size 933 of 1016 vol = 24605.79
core size 929 of 1016 vol = 23893.85
core size 925 of 1016 vol = 23251.22
core size 920 of 1016 vol = 22447.67
core size 916 of 1016 vol = 21886.32
core size 911 of 1016 vol = 21176.49
core size 907 of 1016 vol = 20589.93
core size 903 of 1016 vol = 20055.39
core size 897 of 1016 vol = 19344.6
core size 883 of 1016 vol = 17750.1
core size 878 of 1016 vol = 17034.49
core size 874 of 1016 vol = 16593.69
core size 870 of 1016 vol = 16201.91
core size 866 of 1016 vol = 15862.28
core size 858 of 1016 vol = 15131.45
core size 854 of 1016 vol = 14813.23
core size 850 of 1016 vol = 14464
core size 846 of 1016 vol = 14126.29
core size 838 of 1016 vol = 13504.1
core size 834 of 1016 vol = 13213.07
core size 828 of 1016 vol = 12795.39
core size 822 of 1016 vol = 12345.63
core size 818 of 1016 vol = 12046.17
core size 814 of 1016 vol = 11751.58
core size 804 of 1016 vol = 11055.41
core size 799 of 1016 vol = 10680.23
core size 792 of 1016 vol = 10123.62
core size 785 of 1016 vol = 9548.388
core size 779 of 1016 vol = 9143.99
core size 774 of 1016 vol = 8812.803
core size 767 of 1016 vol = 8388.404
core size 760 of 1016 vol = 7950.566
core size 756 of 1016 vol = 7726.294
core size 749 of 1016 vol = 7326.144
core size 745 of 1016 vol = 7103.338
core size 738 of 1016 vol = 6718.721
core size 734 of 1016 vol = 6500.294
core size 725 of 1016 vol = 6027.433
core size 721 of 1016 vol = 5807.743
core size 716 of 1016 vol = 5540.084
core size 712 of 1016 vol = 5346.957
core size 708 of 1016 vol = 5162.14
core size 703 of 1016 vol = 4939.766
core size 698 of 1016 vol = 4727.702
core size 692 of 1016 vol = 4480.493
core size 688 of 1016 vol = 4313.975
core size 682 of 1016 vol = 4087.702
core size 674 of 1016 vol = 3795.345
core size 670 of 1016 vol = 3633.276
core size 666 of 1016 vol = 3475.45
core size 661 of 1016 vol = 3290.835
core size 657 of 1016 vol = 3147.592
core size 652 of 1016 vol = 2979.985
core size 648 of 1016 vol = 2849.931
core size 643 of 1016 vol = 2693.37
core size 636 of 1016 vol = 2496.804
core size 630 of 1016 vol = 2337.382
core size 626 of 1016 vol = 2230.149
core size 620 of 1016 vol = 2093.185
core size 616 of 1016 vol = 2003.067
core size 612 of 1016 vol = 1921.572
core size 603 of 1016 vol = 1773.238
core size 599 of 1016 vol = 1699.378
core size 595 of 1016 vol = 1634.641
core size 590 of 1016 vol = 1560.77
core size 585 of 1016 vol = 1491.411
core size 581 of 1016 vol = 1438.605
core size 574 of 1016 vol = 1360.622
core size 568 of 1016 vol = 1296.957
core size 563 of 1016 vol = 1246.175
core size 559 of 1016 vol = 1209.404
core size 553 of 1016 vol = 1159.368
core size 546 of 1016 vol = 1101.017
core size 542 of 1016 vol = 1070.545
core size 538 of 1016 vol = 1044.481
core size 532 of 1016 vol = 1009.694
core size 527 of 1016 vol = 979.993
core size 522 of 1016 vol = 953.035
core size 518 of 1016 vol = 932.107
core size 513 of 1016 vol = 907.933
core size 505 of 1016 vol = 869.764
core size 501 of 1016 vol = 848.147
core size 494 of 1016 vol = 816.515
core size 490 of 1016 vol = 794.152
core size 485 of 1016 vol = 770.493
core size 481 of 1016 vol = 751.13
core size 477 of 1016 vol = 732.67
core size 470 of 1016 vol = 705.044
core size 464 of 1016 vol = 679.171
core size 457 of 1016 vol = 649.518
core size 447 of 1016 vol = 609.374
core size 440 of 1016 vol = 575.339
core size 434 of 1016 vol = 548.988
core size 430 of 1016 vol = 531.367
core size 424 of 1016 vol = 507.41
core size 419 of 1016 vol = 488.061
core size 412 of 1016 vol = 461.532
core size 408 of 1016 vol = 442.519
core size 403 of 1016 vol = 423.914
core size 397 of 1016 vol = 402.858
core size 393 of 1016 vol = 387.114
core size 387 of 1016 vol = 367.61
core size 383 of 1016 vol = 352.063
core size 379 of 1016 vol = 338.519
core size 375 of 1016 vol = 326.382
core size 371 of 1016 vol = 313.762
core size 367 of 1016 vol = 301.961
core size 361 of 1016 vol = 285.419
core size 357 of 1016 vol = 273.244
core size 353 of 1016 vol = 262.224
core size 348 of 1016 vol = 249.529
core size 344 of 1016 vol = 239.487
core size 338 of 1016 vol = 226.657
core size 334 of 1016 vol = 218.44
core size 328 of 1016 vol = 207.888
core size 323 of 1016 vol = 197.631
core size 318 of 1016 vol = 188.301
core size 313 of 1016 vol = 180.095
core size 308 of 1016 vol = 172.276
core size 301 of 1016 vol = 163.127
core size 295 of 1016 vol = 155.426
core size 291 of 1016 vol = 150.198
core size 287 of 1016 vol = 145.242
core size 281 of 1016 vol = 138.469
core size 276 of 1016 vol = 133.185
core size 269 of 1016 vol = 126.054
core size 259 of 1016 vol = 117.057
core size 253 of 1016 vol = 111.472
core size 248 of 1016 vol = 106.811
core size 243 of 1016 vol = 102.321
core size 232 of 1016 vol = 93.573
core size 226 of 1016 vol = 87.761
core size 222 of 1016 vol = 84.079
core size 216 of 1016 vol = 79.584
core size 208 of 1016 vol = 73.779
core size 203 of 1016 vol = 69.871
core size 198 of 1016 vol = 66.345
core size 194 of 1016 vol = 63.598
core size 186 of 1016 vol = 59.278
core size 182 of 1016 vol = 56.785
core size 176 of 1016 vol = 53.48
core size 170 of 1016 vol = 50.2
core size 165 of 1016 vol = 47.542
core size 160 of 1016 vol = 44.99
core size 155 of 1016 vol = 42.558
core size 148 of 1016 vol = 39.536
core size 139 of 1016 vol = 35.965
core size 133 of 1016 vol = 33.401
core size 127 of 1016 vol = 31.164
core size 116 of 1016 vol = 27.494
core size 112 of 1016 vol = 25.942
core size 106 of 1016 vol = 23.904
core size 99 of 1016 vol = 21.813
core size 94 of 1016 vol = 20.122
core size 89 of 1016 vol = 18.544
core size 83 of 1016 vol = 16.712
core size 76 of 1016 vol = 14.667
core size 72 of 1016 vol = 13.516
core size 67 of 1016 vol = 12.286
core size 61 of 1016 vol = 10.917
core size 57 of 1016 vol = 9.767
core size 53 of 1016 vol = 8.779
core size 40 of 1016 vol = 6.342
core size 33 of 1016 vol = 4.703
core size 32 of 1016 vol = 4.321
core size 31 of 1016 vol = 4.125
core size 27 of 1016 vol = 3.535
core size 25 of 1016 vol = 3.114
core size 21 of 1016 vol = 2.513
core size 20 of 1016 vol = 2.241
core size 17 of 1016 vol = 1.828
core size 16 of 1016 vol = 1.54
core size 12 of 1016 vol = 1.106
> inds <- print(core, vol=2.241)
# 829 positions (cumulative volume <= 2.241 Angstrom^3)
> inds <- print(core, vol=488.061)
# 903 positions (cumulative volume <= 488.061 Angstrom^3)
As I understand, if the output of print(core, vol=2.241) should be 20 positions, and print(core, vol=488.061) should be 419, right? Or did I miss anything?
My environment is:
sessionInfo() R version 3.5.1 (2018-07-02) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Sierra 10.12.4
Matrix products: default BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages: [1] stats graphics grDevices utils datasets methods base
other attached packages: [1] bio3d_2.3-4.9000
loaded via a namespace (and not attached): [1] compiler_3.5.1 parallel_3.5.1 Rcpp_0.12.17 grid_3.5.1
Thanks! Yong
Comments (4)
-
-
Thanks for reporting. We will check. Can you try with
shortcut=FALSE
and see if it works properly? -
Hi Xin-Qiu,
Thanks for the help. Yes, shortcut=FALSE could solve the issue.
Cheers, Yong
-
- changed status to resolved
- Log in to comment
Thanks for reporting. We will check. Can you try with
shortcut=FALSE
and see if it works properly?