Dear Yimin and CCP4BB readers,
The autoPROC Wiki page mentioned in Clemens's message (below) is being
regularly updated with the results emerging from extending that comparison
to the improved BUILT=20241002 of the 20240630 version of XDS announced in
Kay's message.
With best wishes,
Gerard.
--
On Wed, Oct 02, 2024 at 05:17:56PM +0100, Clemens Vonrhein wrote:
> Dear Yimin,
>
> without wanting to preempt additional feedback that the XDS developers
> might be able to provide (concerning the changes within that July 2024
> XDS version that seem to trigger the differences you see), may we
> suggest that you have a look at
>
>
> https://www.globalphasing.com/autoproc/wiki/index.cgi?ComparisonProcessing202409
>
> Here we have collected a large amount of information and detailed
> comparisons regarding the new 2024 XDS version (that we also shared
> and discussed in detail with the XDS developers over the last weeks)
> ... and just in the last few hours we discovered that (1) a binary for
> the previous 2023 version with an extended lifetime is now available
> at [1], and that (2) a new/modified 2024 version has been published
> with some hints about changes.
>
> We are testing this very latest version (20241002) as we speak and we
> will update the comparison page mentioned above accordingly. So
> ... stay tuned ;-)
>
> Cheers
>
> Clemens
>
> [1] https://xds.mr.mpg.de/
>
> On Wed, Oct 02, 2024 at 04:30:55PM +0200, Yimin Hu 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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