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 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
