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

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