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Re: [ccp4bb]: Reporting Data Statistics !
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Some usefull programs (awk scripts) to extract information from
DENZO/SCALEPACK can be found on Paul Emselys website
(http://www.chem.gla.ac.uk/~paule/denzolog/).
Depending on which version you use you might want to get more up to date
ones on http://www.chem.gla.ac.uk/~bernhard/scalepacklog and
http://www.chem.gla.ac.uk/~bernhard/denzolog resp.!
Although I am not sure if that can answer all your questions!
Bernhard
> I apologize for this non-CCP4 question.
> I am trying to find out the foll. from my scale output file processed
> with Denzo that I would like to report in my publication:
> 1. no. of unique reflections (Is it = 131853 OR 124523 OR 120181 ? See
> below!)
> 3. overall redundancy of the dataset
> Scalepack shows several different numbers all over the logfile and I
> would like to find out the 'correct' numbers to report. I have copied
> various parts of the logfile where this information occurs:
> -------------------------
> Storage required for H list 51 K list 2208 unique reflection list
> ***131853***
> Hkl's refined: 116900 N.Chi**2: 176.463 Decrease: 173.950 * 432819 =
> 7.53E+07
> Hkl's refined: 116900 N.Chi**2: 1.002 Decrease: 0.015 * 432819 =
> 6609.1
> Hkl's refined: 116900 N.Chi**2: 0.984 Decrease: 0.000 * 432819
> = 152.0
> Hkl's refined: 116900 N.Chi**2: 0.983 Decrease: 0.000 * 432819
> = 15.8
> Hkl's refined: 116900 N.Chi**2: 0.983 Decrease: 0.000 * 432819
> = 2.1
> Hkl's refined: 116900 N.Chi**2: 0.983 Decrease: 0.000 * 432819
> = 0.3
> --------------------------
> Shell I/Sigma in resolution shells:
> Lower Upper No. of reflections with I / Sigma less than
> limit limit 0 1 2 3 5 10 20 >20 total
> 100.00 4.94 21 33 43 52 79 184 1720 8160 9880
> 4.94 3.92 14 23 32 45 78 169 1042 8516 9558
> 3.92 3.43 15 26 48 67 134 307 1410 8058 9468
> 3.43 3.11 23 45 88 139 273 643 2169 7279 9448
> 3.11 2.89 58 132 260 387 670 1442 3782 5604 9386
> 2.89 2.72 90 225 433 657 1102 2324 5525 3854 9379
> 2.72 2.58 145 407 757 1092 1760 3451 6884 2466 9350
> 2.58 2.47 206 570 1072 1564 2537 4526 7718 1612 9330
> 2.47 2.38 307 819 1510 2188 3353 5611 8448 846 9294
> 2.38 2.29 420 1223 2182 3109 4491 6762 8920 366 9286
> 2.29 2.22 580 1614 2894 3990 5610 7871 9098 0 9098
> 2.22 2.16 739 2166 3632 4735 6159 7745 8543 48 8591
> 2.16 2.10 889 2482 3959 4954 6008 6940 7339 61 7400
> 2.10 2.05 787 2006 3139 3824 4495 4951 5055 0 5055
> All hkl 4294 11771 20049 26803 36749 52926 77653 46870
> ***124523***
>
> -------------------------------------------------------------------
> MORE NUMBERS FROM MY FINAL *.PDB FILE !!!!!!!
> REMARK theoretical total number of refl. in resol. range: 132446 (
> 100.0 % )
> REMARK number of unobserved reflections (no entry or |F|=0): 12265 (
> 9.3 % )
> REMARK number of reflections rejected: 0 (
> 0.0 % )
> REMARK total number of reflections used:
> ***120181*** ( 90.7 % )
> REMARK number of reflections in working set: 114131 (
> 86.2 % )
> -------------------------------------------------------------------
> Shell Summary of observation redundancies by shells:
> Lower Upper No. of reflections with given No. of observations
> limit limit 0 1 2 3 4 5-6 7-8 9-12 13-19
> >19 total
> 100.00 4.94 23 24 88 138 609 1023 3321 4361 316
> 0 9880
> 4.94 3.92 0 8 34 106 215 846 3478 4654 217
> 0 9558
> 3.92 3.43 0 36 267 260 880 2608 3795 1618 4
> 0 9468
> 3.43 3.11 3 83 427 505 2640 4035 1627 131 0
> 0 9448
> 3.11 2.89 6 78 534 496 4432 3723 123 0 0
> 0 9386
> 2.89 2.72 19 91 546 515 5801 2419 7 0 0
> 0 9379
> 2.72 2.58 19 94 544 502 5854 2353 3 0 0
> 0 9350
> 2.58 2.47 31 77 552 483 5876 2340 2 0 0
> 0 9330
> 2.47 2.38 40 77 537 487 5868 2324 1 0 0
> 0 9294
> 2.38 2.29 54 158 778 1753 4741 1854 2 0 0
> 0 9286
> 2.29 2.22 256 416 1433 2478 3513 1258 0 0 0
> 0 9098
> 2.22 2.16 687 968 2078 2406 2373 765 1 0 0
> 0 8591
> 2.16 2.10 1904 1767 2266 1840 1215 312 0 0 0
> 0 7400
> 2.10 2.05 4284 1887 1612 1125 376 55 0 0 0
> 0 5055
> All hkl 7326 5764 11696 13094 44393 25915 12360 10764 537
> 0 124523
>
> IS THIS THE TABLE THAT ONE USES TO CALCULATE OVERALL REDUNDANCY OF THE
> DATASET ?
> DOES ANYONE KNOW IF SCALEPACK REPORTS IT IN A SIMPLIFIED MANNER
> SOMEPLACE ??
> ---------------------------------------------------------------------------------
> Thanks a ton for your help/comments/suggestions/criticisms!!
> Raji
>
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* Dipl. phys. *
* Bernhard Lohkamp, M.Res. *
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