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/
