Dear Kay, do have any more information or would you mind explaining a bit more
what changes in the XDS code led to these significantly different statistics in
the different XDS versions?
Thanks,John
On Wednesday, October 2, 2024 at 02:35:25 PM CDT, Kay Diederichs
<kay.diederi...@uni-konstanz.de> wrote:
Dear Yimin,
similar shortcomings were observed with other datasets with XDS VERSION Jun 30,
2024 that was posted on July 23 at
https://xds.mr.mpg.de/html_doc/downloading.html . I am sorry for that! The
testing of that version had not uncovered this problem.
Corrected binaries were posted today at that site, and my (admittedly limited)
testing shows them to be as good as, or better than the old (2023) version.
Please install and use these binaries.
That previous version was made available for comparison purposes as
XDS_old.tar.gz, with expiration date 31 Mar 2025, for Linux; download link is
at https://xds.mr.mpg.de/ .
Hope this helps,
Kay
On Wed, 2 Oct 2024 16:30:55 +0200, Yimin Hu <yimin...@tuebingen.mpg.de> wrote:
>Dear colleagues，
>
>I ran into a problem when I reprocessed a dataset after switching to XDS
>VERSION Jun 30, 2024.
>
>Processing the dataset with the old XDS I ended up with these statistics:
>
>RESOLUTION NUMBER OF REFLECTIONS COMPLETENESS R-FACTOR R-FACTOR
>COMPARED I/SIGMA R-meas CC(1/2) Anomal SigAno Nano
> LIMIT OBSERVED UNIQUE POSSIBLE OF DATA observed expected
> Corr
> 5.78 16747 1239 1253 98.9% 7.4% 8.5% 16745
>29.13 7.6% 99.9* 2 0.740 465
> 4.10 29921 2220 2226 99.7% 8.9% 8.7% 29921
>28.12 9.2% 99.8* 9 0.897 951
> 3.35 40065 2848 2849 100.0% 10.1% 9.3%
>40065 23.84 10.4% 99.8* 3 0.841 1264
> 2.91 44213 3390 3390 100.0% 13.5% 13.0% 44213
> 14.61 14.1% 99.8* -10 0.717 1537
> 2.60 54235 3827 3827 100.0% 24.6% 28.4% 54235
> 9.08 25.5% 99.5* -15 0.611 1758
> 2.38 62062 4270 4270 100.0% 42.5% 57.6% 62062
> 5.40 44.1% 98.8* -10 0.565 1973
> 2.20 62076 4589 4589 100.0% 76.3% 111.3%
>62076 3.06 79.2% 97.0* -7 0.549 2138
> 2.06 67437 4941 4941 100.0% 116.7% 176.7% 67437
> 2.03 121.3% 89.2* -8 0.541 2311
> 1.94 70590 5226 5268 99.2% 232.1% 363.5% 70579
> 0.93 241.2% 64.3* -4 0.511 2451
> total 447346 32550 32613 99.8% 12.7% 14.4% 447333
> 9.30 13.2% 99.9* -5 0.621 14848
>
>
>Reprocessing the dataset with the new version I ended up with the following
>statistics though I kept the parameters essentially the same：
>
> RESOLUTION NUMBER OF REFLECTIONS COMPLETENESS R-FACTOR R-FACTOR
> COMPARED I/SIGMA R-meas CC(1/2) Anomal SigAno Nano
> LIMIT OBSERVED UNIQUE POSSIBLE OF DATA observed expected
> Corr
>
> 5.80 16932 1220 1240 98.4% 7.2% 8.5% 16930
>28.65 7.5% 99.9* -39 0.502 459
> 4.12 29888 2207 2209 99.9% 9.9% 9.3% 29888
>25.46 10.3% 99.7* 0 0.707 945
> 3.37 34817 2796 2836 98.6% 14.9% 11.7% 34817
>17.63 15.5% 99.7* 15* 0.947 1244
> 2.92 42552 3268 3347 97.6% 24.5% 23.5% 42552
>10.04 25.5% 99.6* -12 0.583 1481
> 2.61 54120 3811 3816 99.9% 56.8% 69.2% 54120
> 6.14 58.9% 98.2* -14 0.543 1750
> 2.38 60922 4173 4221 98.9% 358.4% 464.1% 60922
> 2.93 371.4% 93.7* -18 0.421 1897
> 2.21 52076 3861 4566 84.6% -99.9% -99.9% 52076
> 0.00 -99.9% 66.9* -37 0.306 1566
> 2.06 40823 3045 4911 62.0% -99.9% -99.9% 40823
> 0.00 -99.9% 33.3* -39 0.196 1047
> 1.95 34764 2526 5227 48.3% -99.9% -99.9% 34764
> 0.00 -99.9% 14.7* -48 0.072 585
> total 366894 26907 32373 83.1% 28.2% 29.1% 366892
> 7.57 29.2% 99.8* -16 0.493 10974
>
>I tried to tweak several parameters, especially for background subtraction,
>but it didn't really help. It would be great if you could give me some
>suggestions. Thank you in advance!
>
>Best,
>Yimin
>
>
>--
>Yimin Hu
>(Pronouns: she/her)
>PhD Student
>Department of Protein Evolution
>Max Planck Institute for Biology, Tübingen
>
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