[buster-discuss] Get Rfree for each resolution bin
Donald Damian Raymond
donal at umich.edu
Thu Mar 12 16:57:10 CET 2015
Hi Clemens,
Thanks for your response. That is exactly what I was looking for. However, there seems to be a discrepancy in the R values reported after running the rvalue program on refine.mtz and the R values in the PDB file. See below for more information.
output from "rvalue refine.mtz"
Using test-set label: FreeR_flag
Using test-set value: 0 (-ifree option)
Using column names FC and FOSC for table of R-values
Resolution --------------- shell average ------------------- ----------------- cumulative --------------------
[A] Nwork Nfree Nall Rwork Rfree Rall Nwork Nfree Nall Rwork Rfree Rall
=======================================================================================================================
44.187 - 12.434 : 645 30 675 0.3287 0.3201 0.3283 645 30 675 0.3287 0.3201 0.3283
12.434 - 9.906 : 642 30 672 0.2405 0.2833 0.2424 1287 60 1347 0.2824 0.3012 0.2832
9.906 - 8.664 : 630 39 669 0.2243 0.2144 0.2237 1917 99 2016 0.2636 0.2662 0.2637
8.664 - 7.877 : 636 34 670 0.2523 0.2341 0.2513 2553 133 2686 0.2612 0.2589 0.2611
7.877 - 7.315 : 648 28 676 0.2504 0.2781 0.2516 3201 161 3362 0.2595 0.2614 0.2596
7.315 - 6.886 : 625 27 652 0.2605 0.3367 0.2632 3826 188 4014 0.2596 0.2685 0.2600
6.886 - 6.542 : 656 37 693 0.2689 0.3236 0.2721 4482 225 4707 0.2607 0.2763 0.2614
6.542 - 6.258 : 657 26 683 0.2731 0.2386 0.2716 5139 251 5390 0.2619 0.2730 0.2624
6.258 - 6.018 : 611 40 651 0.2877 0.2972 0.2883 5750 291 6041 0.2642 0.2758 0.2647
6.018 - 5.810 : 636 31 667 0.2834 0.3674 0.2873 6386 322 6708 0.2657 0.2825 0.2665
5.810 - 5.629 : 648 42 690 0.2718 0.3282 0.2749 7034 364 7398 0.2662 0.2866 0.2672
5.629 - 5.468 : 615 34 649 0.2659 0.3341 0.2693 7649 398 8047 0.2662 0.2901 0.2673
5.468 - 5.325 : 641 27 668 0.2558 0.2755 0.2567 8290 425 8715 0.2653 0.2891 0.2665
5.325 - 5.195 : 629 34 663 0.2541 0.3128 0.2571 8919 459 9378 0.2645 0.2908 0.2658
5.195 - 5.077 : 644 34 678 0.2528 0.2987 0.2551 9563 493 10056 0.2637 0.2914 0.2651
5.077 - 4.969 : 607 37 644 0.2704 0.3070 0.2725 10170 530 10700 0.2641 0.2925 0.2655
4.969 - 4.870 : 631 40 671 0.2608 0.2922 0.2625 10801 570 11371 0.2639 0.2925 0.2654
4.870 - 4.778 : 653 25 678 0.2668 0.3367 0.2694 11454 595 12049 0.2641 0.2946 0.2656
4.778 - 4.693 : 662 37 699 0.2755 0.2872 0.2762 12116 632 12748 0.2648 0.2941 0.2663
4.693 - 4.613 : 592 34 626 0.2615 0.2917 0.2630 12708 666 13374 0.2646 0.2939 0.2661
4.613 - 4.539 : 634 28 662 0.2694 0.2978 0.2707 13342 694 14036 0.2649 0.2941 0.2663
4.539 - 4.469 : 618 38 656 0.2813 0.3963 0.2876 13960 732 14692 0.2657 0.2999 0.2674
4.469 - 4.404 : 659 32 691 0.2842 0.2846 0.2842 14619 764 15383 0.2667 0.2992 0.2683
4.404 - 4.342 : 612 32 644 0.2840 0.3879 0.2892 15231 796 16027 0.2675 0.3032 0.2692
4.342 - 4.283 : 621 35 656 0.2866 0.3384 0.2893 15852 831 16683 0.2683 0.3048 0.2701
4.283 - 4.227 : 647 24 671 0.3013 0.3543 0.3029 16499 855 17354 0.2697 0.3061 0.2715
4.227 - 4.175 : 586 41 627 0.3053 0.2726 0.3032 17085 896 17981 0.2710 0.3046 0.2727
4.175 - 4.124 : 654 33 687 0.3160 0.3481 0.3174 17739 929 18668 0.2728 0.3060 0.2744
4.124 - 4.077 : 649 29 678 0.3244 0.3470 0.3254 18388 958 19346 0.2746 0.3073 0.2762
4.077 - 4.031 : 607 35 642 0.3204 0.3716 0.3232 18995 993 19988 0.2761 0.3095 0.2777
4.031 - 3.987 : 622 33 655 0.3353 0.3528 0.3362 19617 1026 20643 0.2779 0.3108 0.2796
3.987 - 3.945 : 649 31 680 0.3357 0.3335 0.3356 20266 1057 21323 0.2797 0.3115 0.2813
3.945 - 3.905 : 594 31 625 0.3314 0.3110 0.3304 20860 1088 21948 0.2811 0.3115 0.2826
3.905 - 3.866 : 601 32 633 0.3308 0.3129 0.3299 21461 1120 22581 0.2824 0.3115 0.2839
3.866 - 3.829 : 675 41 716 0.3485 0.3846 0.3506 22136 1161 23297 0.2843 0.3140 0.2858
3.829 - 3.793 : 614 27 641 0.3410 0.4379 0.3449 22750 1188 23938 0.2858 0.3166 0.2873
3.793 - 3.759 : 635 41 676 0.3581 0.3924 0.3602 23385 1229 24614 0.2877 0.3191 0.2892
3.759 - 3.726 : 626 35 661 0.3768 0.3175 0.3737 24011 1264 25275 0.2899 0.3191 0.2913
3.726 - 3.693 : 622 23 645 0.3727 0.3615 0.3723 24633 1287 25920 0.2919 0.3198 0.2933
3.693 - 3.662 : 597 34 631 0.3760 0.3682 0.3756 25230 1321 26551 0.2937 0.3209 0.2950
3.662 - 3.632 : 646 27 673 0.3929 0.4591 0.3957 25876 1348 27224 0.2959 0.3236 0.2973
3.632 - 3.603 : 587 37 624 0.3895 0.4087 0.3906 26463 1385 27848 0.2979 0.3258 0.2993
3.603 - 3.575 : 645 34 679 0.3852 0.5102 0.3907 27108 1419 28527 0.2998 0.3294 0.3012
3.575 - 3.548 : 633 44 677 0.4040 0.3538 0.4009 27741 1463 29204 0.3020 0.3300 0.3034
3.548 - 3.521 : 628 30 658 0.4188 0.4693 0.4215 28369 1493 29862 0.3044 0.3331 0.3058
3.521 - 3.496 : 611 34 645 0.4190 0.3919 0.4176 28980 1527 30507 0.3065 0.3342 0.3079
3.496 - 3.471 : 594 38 632 0.4009 0.4583 0.4043 29574 1565 31139 0.3082 0.3369 0.3096
3.471 - 3.447 : 607 32 639 0.4046 0.3350 0.4013 30181 1597 31778 0.3099 0.3369 0.3112
3.447 - 3.423 : 586 27 613 0.4045 0.3554 0.4025 30767 1624 32391 0.3114 0.3371 0.3127
3.423 - 3.400 : 547 24 571 0.4120 0.4855 0.4152 31314 1648 32962 0.3128 0.3390 0.3141
=======================================================================================================================
44.187 - 3.400 : 31314 1648 32962 0.3128 0.3390 0.3141
Refinemet summary in refine.pdb
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : BUSTER 2.10.2
REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER,
REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN,WOMACK;
REMARK 3 : MATTHEWS,TEN EYCK,TRONRUD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.40
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.21
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.0
REMARK 3 COMPLETENESS FOR RANGE (%) : 97.59
REMARK 3 NUMBER OF REFLECTIONS : 32962
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT
REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
REMARK 3 R VALUE (WORKING + TEST SET) : 0.2401
REMARK 3 R VALUE (WORKING SET) : 0.2389
REMARK 3 FREE R VALUE : 0.2632
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.00
REMARK 3 FREE R VALUE TEST SET COUNT : 1648
REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 17
REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 3.40
REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 3.50
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.59
REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2678
REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2030
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2544
REMARK 3 BIN R VALUE (WORKING SET) : 0.2019
REMARK 3 BIN FREE R VALUE : 0.2248
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.00
REMARK 3 BIN FREE R VALUE TEST SET COUNT : 134
REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL
The R factors seem different unless I'm not reading it right.
Best,
Donald
On Mar 10, 2015, at 12:50 PM, Clemens Vonrhein <vonrhein at globalphasing.com> wrote:
> Hi Donald,
>
> On Tue, Mar 10, 2015 at 11:54:17AM -0400, Donald Damian Raymond wrote:
>> Hello buster developers,
>>
>> It is possible to view the R and Rfree for each resolution bin after
>> refinement? Thanks in advance.
>
> Yes: each refinement big cycle will have produced a file R_Rfree.mtv
> that can be viewed with plotmtv (which is part of your BUSTER
> installation). E.g.
>
> % refine ... -d 01 | tee 01.lis
> % plotmtv 01/01-BUSTER/Cycle-5/shell.01/R_Rfree.mtv
>
> If you prefer a more tabular view:
>
> % firefox 01/01-BUSTER/Cycle-5/shell.01/R_Rfree.html
>
> or some other browser. You could also use the 'rvalue' helper to
> list R/Rfree in the individual bins and cumulatively:
>
> % rvalue 01/refine.mtz
>
> For details please see
>
> % rvalue -h
>
> Cheers
>
> Clemens, Claus & Gerard (for buster-develop)
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