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