Hi John, good idea in principle, but the amount of incompatible code changes between versions is surprisingly large. On top of that, XDS philosophy has always been that there is a single "best" algorithm (which may be fine-tuned in subsequent releases). The main arguments for that are: - it is scientifically more satisfactory - it is a support nightmare to have more than one versions/ algorithms.
Best, Kay On Sat, 5 Oct 2024 14:38:22 -0500, john bacik <thesupremecrul...@gmail.com> wrote: >Hi Kay, thank you so much for the explanation, this is very helpful. Maybe >it is already possible, but perhaps the user could select whether to do the >background estimation using either the old or new way (with or without >local fitting), via the XDS.INP file? > >Thanks again, >John > >On Sat, Oct 5, 2024 at 11:27 AM Kay Diederichs < >kay.diederi...@uni-konstanz.de> wrote: > >> Dear John, >> >> version 202406030 of XDS estimates the background "under" a reflection in >> a different way than 20230630 and earlier. >> The new way uses a background template based on the background image >> constructed in the INIT step of XDS, whereas in the old way that was only >> used for calculating a scale factor for INTEGRATE. >> BUILTs 20240723 and 20241002 differ in the way they use the background >> template, and 20241002 does it more subtly, by local fitting, which gives >> more accurate results, but may use more computing time. >> >> Hope this helps, >> Kay >> >> On Sat, 5 Oct 2024 13:45:59 +0000, John Bacik <mx...@yahoo.com> wrote: >> >> > 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 >> >> >> >>######################################################################## >> >> >> >>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/ >> > >> >######################################################################## >> > >> >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/ >> > >> > >> >######################################################################## >> > >> >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/ >> >> ######################################################################## >> >> 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/ >> > >######################################################################## > >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/ > ######################################################################## 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/
